Hello Zhiyu--
>
> protocol.loadPDB("5jzr_autopsf_center_his.pdb",deleteUnknownAtoms=True)
>
> In the 5jzr_xxxx.pdb file, there are coordinate information for
> histidine #100 (I can open this pdb properly in pymol or chimera),
> as following:
>
> ATOM 1522 N HIS A 100 2.433 -7.437 0.132 1.00 0.00 N
>
> However, using this pdb as an input, there is no histidine in the
> output .sa file. I have tried nomenclature HIS, HISE, HISD, HSE, but
> none of the input generate an output histidine, therefore I got a
> kink in the calculated structure.
>
You would have to send your PDB. The PDB's 5jzr gives me:
% xplor -py
Xplor-NIH version 3.6.3
C.D. Schwieters, J.J. Kuszewski, Progr. NMR Spectr. 48, 47-62 (2006).
N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003).
https://bit.niddk.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger
User: schwitrs on: eggshell (Linux_x86_64 ) at: 15-Feb-23 10:12:40
python> import protocol
python> protocol.loadPDB('5jzr.pdb',deleteUnknownAtoms=True)
loading pdb file: 5jzr.pdb [psf] PDBTool:read: atom not found in structure: A
MET 1 H
python> for atom in AtomSel("resid 100"):
pyth01> print(atom.string(), atom.pos())
pyth01>
A 100 HIS N [ 6.277, 20.273, -11.286]
A 100 HIS HN [ 6.866, 19.806, -11.915]
A 100 HIS CA [ 4.847, 19.988, -11.305]
A 100 HIS HA [ 4.321, 20.931, -11.324]
A 100 HIS CB [ 4.481, 19.189, -12.556]
A 100 HIS HB1 [ 5.062, 19.553, -13.391]
A 100 HIS HB2 [ 3.431, 19.325, -12.768]
A 100 HIS CG [ 4.735, 17.719, -12.423]
A 100 HIS ND1 [ 5.616, 17.032, -13.230]
A 100 HIS HD1 [ 6.151, 17.419, -13.954]
A 100 HIS CD2 [ 4.219, 16.805, -11.568]
A 100 HIS HD2 [ 3.491, 16.992, -10.791]
A 100 HIS CE1 [ 5.630, 15.758, -12.880]
A 100 HIS HE1 [ 6.226, 14.982, -13.337]
A 100 HIS NE2 [ 4.791, 15.594, -11.873]
A 100 HIS C [ 4.430, 19.219, -10.055]
A 100 HIS O [ 3.255, 19.203, -9.685]
i.e. it works fine. So, either your input PDB differs here, or
something else is going on.
I can say that the PDB snippet you sent, starting with:
ATOM 1522 N HIS A 100 2.433 -7.437 0.132 1.00 0.00 N
has misaligned columns: there should be two extra spaces after the
ATOM specifier, but this problem may be due to an email miscommunication.
Charles
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