Hi Charles,
Thanks for the tip. I am running into weird error now.
The command protocol.initCoords(fileName) does not recognize any of the
atoms while protocol.loadPDB(fileName) loads the pdb file correctly. It
does not make sense as protocol.loadPDB internally calls initCoords [As I
see from the code].
Clip from my terminal:
>xplor -py
python> protocol.initCoords('model.pdb')
PDBTool:read: atom not found in structure: MET 1 N
PDBTool:read: atom not found in structure: MET 1 H1
PDBTool:read: atom not found in structure: MET 1 H2
PDBTool:read: atom not found in structure: MET 1 H3
PDBTool:read: atom not found in structure: MET 1 CA
PDBTool:read: atom not found in structure: MET 1 HA
PDBTool:read: atom not found in structure: MET 1 CB
PDBTool:read: atom not found in structure: MET 1 HB1 ..........
matchInexactAtomEntry: found no match for entry 1 N
matchInexactAtomEntry: found no match for entry 1 H1
matchInexactAtomEntry: found no match for entry 1 H2
matchInexactAtomEntry: found no match for entry 1 H3
matchInexactAtomEntry: found no match for entry 1 CA
matchInexactAtomEntry: found no match for entry 1 HA
matchInexactAtomEntry: found no match for entry 1 CB
matchInexactAtomEntry: found no match for entry 1 HB1 .........
File "/home/vsvammi/programs/xplor/python/protocol.py", line 639, in
initCoords
unreadEntries)
Exception: too many unreadable ATOM entries: 1231
While protocol.loadPDB works perfectly. Can you please suggest whats going
wrong. The first residue of the PDB file looks this:
ATOM 1 N MET 1 27.959 25.584 17.774 1.00 0.00
ATOM 2 H1 MET 1 27.970 24.816 17.118 1.00 0.00
ATOM 3 H2 MET 1 28.726 26.167 17.471 1.00 0.00
ATOM 4 H3 MET 1 28.248 25.201 18.662 1.00 0.00
ATOM 5 CA MET 1 26.757 26.425 17.888 1.00 0.00
ATOM 6 HA MET 1 26.536 26.725 16.864 1.00 0.00
ATOM 7 CB MET 1 25.497 25.747 18.427 1.00 0.00
ATOM 8 HB1 MET 1 24.666 26.395 18.149 1.00 0.00
ATOM 9 HB2 MET 1 25.286 24.819 17.896 1.00 0.00
ATOM 10 CG MET 1 25.374 25.581 19.942 1.00 0.00
ATOM 11 HG1 MET 1 26.264 25.075 20.316 1.00 0.00
ATOM 12 HG2 MET 1 25.329 26.565 20.410 1.00 0.00
ATOM 13 SD MET 1 23.894 24.731 20.544 1.00 0.00
ATOM 14 CE MET 1 24.249 24.851 22.315 1.00 0.00
ATOM 15 HE1 MET 1 23.798 24.026 22.866 1.00 0.00
ATOM 16 HE2 MET 1 25.321 24.814 22.509 1.00 0.00
ATOM 17 HE3 MET 1 23.918 25.787 22.765 1.00 0.00
ATOM 18 C MET 1 27.082 27.661 18.715 1.00 0.00
ATOM 19 O MET 1 27.796 27.549 19.709 1.00 0.00
Thanks
Santhosh
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