Ensemble Analysis

This example compares experimental structural data analyzed using Principal Component Analysis (PCA) with the theoretical data predicted by Anisotropic Network Model (ANM):

Reference

Bakan A, Bahar I. The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci U S A. 2009 106(34):14349-54.

Retrieve dataset

In [1]:
from prody import *
from pylab import *
%matplotlib inline
//anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
In [2]:
p38 = parsePDB('1p38')
@> PDB file is found in working directory (1p38.pdb.gz).
@> 2962 atoms and 1 coordinate set(s) were parsed in 0.06s.
In [3]:
p38_sequence = p38.getHierView()['A'].getSequence()
In [4]:
p38_sequence
Out[4]:
'ERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGHRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLAQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLD'
In [5]:
blast_record = blastPDB(p38_sequence)
@> Blast searching NCBI PDB database for "ERPTF..."
@> Blast search completed in 6.5s.
In [6]:
pdbids = blast_record.getHits()
In [7]:
pdbfiles = fetchPDB(*pdbids, compressed=False)

Set reference chain

In [8]:
ref_structure = parsePDB('1p38')
ref_selection = ref_structure.select('resnum 5 to 31 36 to 114 122 to '
                                     '169 185 to 351 and calpha')
@> PDB file is found in working directory (1p38.pdb.gz).
@> 2962 atoms and 1 coordinate set(s) were parsed in 0.09s.
In [9]:
ref_chain = ref_selection.getHierView().getChain('A')
repr(ref_chain)
Out[9]:
'<Chain: A from 1p38 (321 residues, 321 atoms)>'

Ensemble Preparation

In [10]:
ensemble = PDBEnsemble('p38 X-ray')
In [11]:
ensemble.setAtoms(ref_chain)
ensemble.setCoords(ref_chain)
In [12]:
for pdbfile in pdbfiles:
    structure = parsePDB(pdbfile, subset='calpha')
    mappings = mapOntoChain(structure, ref_chain)
    atommap = mappings[0][0]
    ensemble.addCoordset(atommap, weights=atommap.getFlags('mapped'), degeneracy=True)
@> 356 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1yqj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1yqj_ca (len=356) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 90% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4e5a_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain X from 4e5a_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2i0h_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2i0h_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3gi3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3gi3_ca (len=330) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 96% overlap.
@> 675 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 4kip_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4kip_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@>   Comparing Chain B from 4kip_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 1352 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 4kiq_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4kiq_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain B from 4kiq_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain C from 4kiq_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain D from 4kiq_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1m7q_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1m7q_ca (len=348) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 346 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3zya_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3zya_ca (len=346) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 1di9_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1di9_ca (len=348) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 321 atoms and 1 coordinate set(s) were parsed in 0.05s.
@> Evaluating AtomGroup 3ody_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain X from 3ody_ca (len=321) with Chain A from 1p38:
@> 	Mapped: 306 residues match with 99% sequence identity and 95% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3pg3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3pg3_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 346 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3fkn_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fkn_ca (len=346) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 343 atoms and 1 coordinate set(s) were parsed in 0.08s.
@> Evaluating AtomGroup 3fko_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fko_ca (len=343) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 3fkl_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fkl_ca (len=344) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 329 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3hec_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hec_ca (len=329) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 97% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 1a9u_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1a9u_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 1384 atoms and 1 coordinate set(s) were parsed in 0.12s.
@> Evaluating AtomGroup 3ds6_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3ds6_ca (len=343) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@>   Comparing Chain B from 3ds6_ca (len=343) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@>   Comparing Chain C from 3ds6_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@>   Comparing Chain D from 3ds6_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 4eh8_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4eh8_ca (len=336) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 326 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 2fsm_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain X from 2fsm_ca (len=326) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 98% overlap.
@> 333 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3heg_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3heg_ca (len=333) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 325 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 2fso_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain X from 2fso_ca (len=325) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 98% overlap.
@> 342 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3fsk_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fsk_ca (len=342) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3kq7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3kq7_ca (len=348) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3oc1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3oc1_ca (len=330) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 5tbe_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 5tbe_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 318 residues match with 99% sequence identity and 95% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3s3i_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3s3i_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 338 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3bv3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3bv3_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3hl7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hl7_ca (len=336) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=5%, overlap=95%).
@> Trying to map atoms based on global sequence alignment:
@>   Comparing Chain A from 3hl7_ca (len=336) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3e93_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3e93_ca (len=347) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3e92_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3e92_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 357 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3itz_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3itz_ca (len=357) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 89% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3bv2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3bv2_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 1356 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 4kin_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4kin_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain B from 4kin_ca (len=341) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain C from 4kin_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain D from 4kin_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@> 338 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3gcv_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3gcv_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 94% overlap.
@> 324 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 2fst_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain X from 2fst_ca (len=324) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 98% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4eh7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4eh7_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 4ewq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4ewq_ca (len=347) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2puu_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2puu_ca (len=330) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 96% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3gcs_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3gcs_ca (len=331) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 96% overlap.
@> 333 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3lfb_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3lfb_ca (len=333) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 98% sequence identity and 96% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3nnw_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3nnw_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3fc1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain X from 3fc1_ca (len=330) with Chain A from 1p38:
@> 	Mapped: 316 residues match with 99% sequence identity and 95% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3mh0_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3mh0_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3d7z_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3d7z_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4ka3_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4ka3_ca (len=340) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 94% overlap.
@>   Comparing Chain B from 4ka3_ca (len=8) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3hll_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hll_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 94% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3flw_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3flw_ca (len=345) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 92% overlap.
@> 343 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fls_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fls_ca (len=343) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 93% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3flq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3flq_ca (len=345) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 1471 atoms and 1 coordinate set(s) were parsed in 0.17s.
@> Evaluating AtomGroup 4loq_ca: 8 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4loq_ca (len=352) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@>   Comparing Chain B from 4loq_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@>   Comparing Chain C from 4loq_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 308 residues match with 100% sequence identity and 91% overlap.
@>   Comparing Chain D from 4loq_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@>   Comparing Chain M from 4loq_ca (len=18) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@>   Comparing Chain L from 4loq_ca (len=22) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@>   Comparing Chain K from 4loq_ca (len=22) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@>   Comparing Chain N from 4loq_ca (len=18) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> 1472 atoms and 1 coordinate set(s) were parsed in 0.14s.
@> Evaluating AtomGroup 4lop_ca: 8 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4lop_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@>   Comparing Chain B from 4lop_ca (len=350) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@>   Comparing Chain C from 4lop_ca (len=341) with Chain A from 1p38:
@> 	Mapped: 311 residues match with 100% sequence identity and 91% overlap.
@>   Comparing Chain D from 4lop_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@>   Comparing Chain K from 4lop_ca (len=21) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@>   Comparing Chain L from 4lop_ca (len=21) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@>   Comparing Chain M from 4lop_ca (len=18) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@>   Comparing Chain N from 4lop_ca (len=19) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> 326 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 4geo_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4geo_ca (len=326) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 97% sequence identity and 98% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1r39_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1r39_ca (len=345) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fly_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fly_ca (len=347) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3hp5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hp5_ca (len=330) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 96% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2bal_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2bal_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@> 370 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4loo_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4loo_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@>   Comparing Chain B from 4loo_ca (len=21) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3gcq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3gcq_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 343 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fln_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain C from 3fln_ca (len=343) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 93% overlap.
@> 327 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4e8a_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4e8a_ca (len=327) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 97% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3uvr_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3uvr_ca (len=331) with Chain A from 1p38:
@> 	Mapped: 317 residues match with 99% sequence identity and 95% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3uvp_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3uvp_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 333 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3uvq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3uvq_ca (len=333) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1ove_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1ove_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 328 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1ian_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1ian_ca (len=328) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 97% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3odz_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain X from 3odz_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@> 338 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1ywr_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1ywr_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3iw6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3iw6_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2ewa_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2ewa_ca (len=330) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3hv3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hv3_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 2y8o_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2y8o_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain B from 2y8o_ca (len=8) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=12%, overlap=2%).
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3gcp_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3gcp_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4f9w_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4f9w_ca (len=336) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4f9y_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4f9y_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 341 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3hp2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hp2_ca (len=341) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 359 atoms and 10 coordinate set(s) were parsed in 0.11s.
@> Evaluating AtomGroup 2lgc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2lgc_ca (len=359) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 89% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fl4_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fl4_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 94% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3iw5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3iw5_ca (len=336) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3hrb_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hrb_ca (len=344) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 93% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3iw7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3iw7_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3u8w_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3u8w_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3iw8_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3iw8_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 96% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4r3c_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4r3c_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1bl7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1bl7_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1bl6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1bl6_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1bmk_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1bmk_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> 678 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3mvl_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3mvl_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain B from 3mvl_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 667 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 3mvm_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3mvm_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@>   Comparing Chain B from 3mvm_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 342 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fml_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fml_ca (len=342) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 93% overlap.
@> 346 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fmm_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fmm_ca (len=346) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 341 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fmn_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fmn_ca (len=341) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fmh_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fmh_ca (len=347) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fmj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fmj_ca (len=344) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 326 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 5ml5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 5ml5_ca (len=326) with Chain A from 1p38:
@> 	Mapped: 315 residues match with 99% sequence identity and 96% overlap.
@> 338 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3c5u_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3c5u_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3kf7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3kf7_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 94% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2fsl_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain X from 2fsl_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 1307 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 2onl_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2onl_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain C from 2onl_ca (len=317) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=4%, overlap=78%).
@>   Comparing Chain B from 2onl_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain D from 2onl_ca (len=313) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=4%, overlap=77%).
@> 355 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 5etc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 5etc_ca (len=355) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 90% overlap.
@> 703 atoms and 1 coordinate set(s) were parsed in 0.07s.
@> Evaluating AtomGroup 5eta_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain B from 5eta_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@>   Comparing Chain D from 5eta_ca (len=16) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=2%).
@>   Comparing Chain A from 5eta_ca (len=336) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@>   Comparing Chain C from 5eta_ca (len=16) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=2%).
@> 348 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 1ouk_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1ouk_ca (len=348) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 341 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1yw2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1yw2_ca (len=341) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> Trying to map atoms based on global sequence alignment:
@>   Comparing Chain A from 1yw2_ca (len=341) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 94% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3new_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3new_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 352 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3gfe_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3gfe_ca (len=352) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 340 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 1wfc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1wfc_ca (len=340) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 93% overlap.
@> 350 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1ouy_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1ouy_ca (len=350) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 4a9y_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4a9y_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 346 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 5etf_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 5etf_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain B from 5etf_ca (len=8) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=2%).
@> 341 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3lhj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3lhj_ca (len=341) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 329 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2baq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2baq_ca (len=329) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3p7a_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3p7a_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3nnu_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3nnu_ca (len=348) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2ghm_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2ghm_ca (len=336) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 95% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2zaz_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2zaz_ca (len=345) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3nnv_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3nnv_ca (len=348) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2ghl_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2ghl_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3p78_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3p78_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3p79_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3p79_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 341 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2gtm_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2gtm_ca (len=341) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 94% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3nnx_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3nnx_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2gtn_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2gtn_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 95% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3mpa_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3mpa_ca (len=331) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3obg_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3obg_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3l8s_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3l8s_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 96% overlap.
@> 342 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3ha8_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3ha8_ca (len=342) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 326 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3s4q_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3s4q_ca (len=326) with Chain A from 1p38:
@> 	Mapped: 315 residues match with 99% sequence identity and 96% overlap.
@> 325 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1kv2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1kv2_ca (len=325) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 98% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3obj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3obj_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 1kv1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1kv1_ca (len=331) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 342 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3mw1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3mw1_ca (len=342) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 93% overlap.
@> 726 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2okr_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2okr_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain C from 2okr_ca (len=24) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@>   Comparing Chain D from 2okr_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain F from 2okr_ca (len=24) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> 335 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3lff_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3lff_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3mpt_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3mpt_ca (len=347) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3o8p_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3o8p_ca (len=336) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1lew_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1lew_ca (len=341) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 94% overlap.
@>   Comparing Chain B from 1lew_ca (len=10) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=2%).
@> 326 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2npq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2npq_ca (len=326) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 98% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4zth_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4zth_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 340 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3zs5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3zs5_ca (len=340) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 329 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3k3j_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3k3j_ca (len=329) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3p7b_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3p7b_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3p7c_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3p7c_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1lez_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1lez_ca (len=343) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 93% overlap.
@>   Comparing Chain B from 1lez_ca (len=8) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=2%).
@> 334 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3lfc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3lfc_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 98% sequence identity and 95% overlap.
@> 329 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3mgy_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3mgy_ca (len=329) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3flz_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3flz_ca (len=347) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2yix_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2yix_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 355 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 5eti_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 5eti_ca (len=355) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 90% overlap.
@> 464 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 3tg1_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3tg1_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@>   Comparing Chain B from 3tg1_ca (len=130) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=36%).
@> 325 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2yis_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2yis_ca (len=325) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 98% overlap.
@> 325 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2yiw_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2yiw_ca (len=325) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 98% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3zsh_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3zsh_ca (len=331) with Chain A from 1p38:
@> 	Mapped: 317 residues match with 99% sequence identity and 95% overlap.
@> 326 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3zsi_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3zsi_ca (len=326) with Chain A from 1p38:
@> 	Mapped: 316 residues match with 99% sequence identity and 96% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2gfs_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2gfs_ca (len=344) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3mh1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3mh1_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3mh2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3mh2_ca (len=330) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3mh3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3mh3_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3zsg_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3zsg_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1r3c_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1r3c_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 357 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3py3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3py3_ca (len=357) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 89% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3o8t_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3o8t_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3oef_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain X from 3oef_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 318 residues match with 99% sequence identity and 95% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3ctq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3ctq_ca (len=336) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 346 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fmk_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fmk_ca (len=346) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3p4k_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3p4k_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain P from 3p4k_ca (len=11) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=0%, overlap=3%).
@> 343 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3que_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3que_ca (len=343) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3qud_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3qud_ca (len=345) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 326 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3l8x_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3l8x_ca (len=326) with Chain A from 1p38:
@> 	Mapped: 313 residues match with 99% sequence identity and 96% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3lfe_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3lfe_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 96% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3lfd_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3lfd_ca (len=331) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 98% sequence identity and 96% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fi4_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fi4_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 94% overlap.
@> 327 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 5tco_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 5tco_ca (len=327) with Chain A from 1p38:
@> 	Mapped: 316 residues match with 99% sequence identity and 96% overlap.
@> 333 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3lfa_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3lfa_ca (len=333) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 333 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2rg5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2rg5_ca (len=333) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3o8u_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3o8u_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3rin_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3rin_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2rg6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2rg6_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3hub_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hub_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3huc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3huc_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2bak_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2bak_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2baj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2baj_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 310 residues match with 99% sequence identity and 91% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3d83_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3d83_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3hv7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hv7_ca (len=330) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 343 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 5uoj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 5uoj_ca (len=343) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 93% overlap.
@> 678 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3hv5_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hv5_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain B from 3hv5_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 677 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3hv4_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hv4_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain B from 3hv4_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1zyj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1zyj_ca (len=331) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3od6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain X from 3od6_ca (len=344) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 93% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3hv6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hv6_ca (len=331) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 340 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3fsf_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3fsf_ca (len=340) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 4aa4_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4aa4_ca (len=347) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 340 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> Evaluating AtomGroup 4aa5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4aa5_ca (len=340) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 4eh9_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4eh9_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1zz2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1zz2_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 328 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4aa0_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4aa0_ca (len=328) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 97% overlap.
@> 329 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4eh5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4eh5_ca (len=329) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 97% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4eh4_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4eh4_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 676 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3gcu_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3gcu_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@>   Comparing Chain B from 3gcu_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4eh6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4eh6_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 324 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4e5b_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4e5b_ca (len=324) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 98% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1w7h_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1w7h_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4eh3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4eh3_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 4eh2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4eh2_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1wbn_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1wbn_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1wbo_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1wbo_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3p5k_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3p5k_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2zb0_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2zb0_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2zb1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2zb1_ca (len=345) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 92% overlap.
@> 327 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3hvc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3hvc_ca (len=327) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 98% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3iph_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3iph_ca (len=347) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1w82_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1w82_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1w83_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1w83_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 1w84_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1w84_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2qd9_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2qd9_ca (len=330) with Chain A from 1p38:
@> 	Mapped: 319 residues match with 99% sequence identity and 96% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4l8m_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4l8m_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 672 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2oza_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 2oza_ca (len=332) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=4%, overlap=81%).
@>   Comparing Chain B from 2oza_ca (len=340) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 100% sequence identity and 94% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1wbv_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1wbv_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 1wbw_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1wbw_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 1wbt_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1wbt_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4fa2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4fa2_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 3k3i_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3k3i_ca (len=332) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 1wbs_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1wbs_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 350 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 5lar_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 5lar_ca (len=350) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1oz1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1oz1_ca (len=344) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3ocg_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3ocg_ca (len=336) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4dli_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4dli_ca (len=334) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 4dlj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4dlj_ca (len=336) with Chain A from 1p38:
@> 	Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@> 350 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4aac_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4aac_ca (len=350) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 3nww_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3nww_ca (len=339) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 338 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3bx5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3bx5_ca (len=338) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 1zzl_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 1zzl_ca (len=351) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3roc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3roc_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 674 atoms and 1 coordinate set(s) were parsed in 0.06s.
@> Evaluating AtomGroup 4tyh_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4tyh_ca (len=339) with Chain A from 1p38:
@> 	Failed to match chains based on residue numbers (seqid=4%, overlap=79%).
@>   Comparing Chain B from 4tyh_ca (len=335) with Chain A from 1p38:
@> 	Mapped: 315 residues match with 100% sequence identity and 94% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4e6c_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4e6c_ca (len=330) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 324 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 4e6a_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4e6a_ca (len=324) with Chain A from 1p38:
@> 	Mapped: 318 residues match with 99% sequence identity and 98% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.05s.
@> Evaluating AtomGroup 3gc7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3gc7_ca (len=349) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 4ehv_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 4ehv_ca (len=337) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 356 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3dt1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@>   Comparing Chain A from 3dt1_ca (len=356) with Chain A from 1p38:
@> 	Mapped: 321 residues match with 99% sequence identity and 90% overlap.
In [13]:
repr(ensemble)
Out[13]:
'<PDBEnsemble: p38 X-ray (237 conformations; 321 atoms)>'
In [14]:
print len(ensemble) == len(pdbfiles)
True
In [15]:
ensemble.iterpose()
@> Starting iterative superposition:
@> Step #1: RMSD difference = 8.4531e-01
@> Step #2: RMSD difference = 2.6130e-04
@> Step #3: RMSD difference = 1.9097e-07
@> Iterative superposition completed in 0.31s.
@> Final superposition to calculate transformations.
@> Superposition completed in 0.06 seconds.

PCA calculation

In [16]:
pca = PCA('p38 xray')           # Instantiate a PCA instance

pca.buildCovariance(ensemble)   # Build covariance for the ensemble

pca.calcModes()                 # Calculate modes (20 of the by default)
@> Covariance is calculated using 237 coordinate sets.
@> Covariance matrix calculated in 0.064546s.
@> 20 modes were calculated in 0.13s.

ANM calculation

In [17]:
anm = ANM('1p38')             # Instantiate a ANM instance

anm.buildHessian(ref_chain)   # Build Hessian for the reference chain

anm.calcModes()               # Calculate slowest non-trivial 20 modes
@> Hessian was built in 0.20s.
@> 20 modes were calculated in 0.12s.

Save your work

In [18]:
saveModel(pca)
saveModel(anm)
saveEnsemble(ensemble)
Out[18]:
'p38_ref_chain.pdb'

Fractional Variance

In [19]:
for mode in pca[:3]:    # Print % variance explained by top PCs
    var = calcFractVariance(mode)*100
    print('{0:s}  % variance = {1:.2f}'.format(mode, var))
Mode 1 from PCA p38 xray  % variance = 24.28
Mode 2 from PCA p38 xray  % variance = 17.52
Mode 3 from PCA p38 xray  % variance = 14.00

Collectivity of modes

In [20]:
for mode in pca[:3]:    # Print PCA mode collectivity
    coll = calcCollectivity(mode)
    print('{0:s}  collectivity = {1:.2f}'.format(mode, coll))
Mode 1 from PCA p38 xray  collectivity = 0.51
Mode 2 from PCA p38 xray  collectivity = 0.17
Mode 3 from PCA p38 xray  collectivity = 0.64
In [21]:
for mode in anm[:3]:    # Print ANM mode collectivity
    coll = calcCollectivity(mode)
    print('{0:s}  collectivity = {1:.2f}'.format(mode, coll))
Mode 1 from ANM 1p38  collectivity = 0.65
Mode 2 from ANM 1p38  collectivity = 0.55
Mode 3 from ANM 1p38  collectivity = 0.68

PCA - ANM overlap

In [22]:
printOverlapTable(pca[:3], anm[:3]) # Top 3 PCs vs slowest 3 ANM modes
Overlap Table
                        ANM 1p38
                    #1     #2     #3
PCA p38 xray #1   -0.77  -0.01  -0.48
PCA p38 xray #2   -0.33  +0.08  +0.41
PCA p38 xray #3   -0.29  -0.70  +0.34

In [23]:
showOverlapTable(pca[:6], anm[:6]);
title('PCA - ANM Overlap Table');
In [24]:
showOverlap(pca[0], anm);
In [25]:
showCumulOverlap(pca[0], anm);

Square Fluctuations

In [26]:
showSqFlucts(pca[:3]);
In [27]:
showSqFlucts(anm[:3]);
In [28]:
showScaledSqFlucts(pca[0], anm[2]);
legend();
In [29]:
showNormedSqFlucts(pca[0], anm[1]);
legend();

Cross Correlations

In [30]:
showCrossCorr(anm)
Out[30]:
(<matplotlib.image.AxesImage at 0x10f9c5350>,
 <matplotlib.colorbar.Colorbar at 0x10e8e30d0>)
In [31]:
showCrossCorr(pca)
Out[31]:
(<matplotlib.image.AxesImage at 0x10fe64490>,
 <matplotlib.colorbar.Colorbar at 0x10fea6b10>)

Preparation of VMD Output

In [32]:
writeNMD('p38_anm.nmd',anm,ref_chain)
Out[32]:
'p38_anm.nmd'
In [33]:
writeNMD('p38_pca.nmd',pca,ref_chain)
Out[33]:
'p38_pca.nmd'
In [ ]: