Dear xplor master,
I used the following command to generate the model:
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
ATOM 1523 HN HIS A 100 3.268 -7.313 -0.401 1.00 0.00 H
ATOM 1524 CA HIS A 100 1.971 -6.254 0.851 1.00 0.00 C
ATOM 1525 HA HIS A 100 2.011 -6.470 1.908 1.00 0.00 H
ATOM 1526 CB HIS A 100 2.883 -5.062 0.551 1.00 0.00 C
ATOM 1527 HB1 HIS A 100 2.865 -4.934 -0.441 1.00 0.00 H
ATOM 1528 HB2 HIS A 100 3.874 -5.275 0.918 1.00 0.00 H
ATOM 1529 ND1 HIS A 100 1.549 -2.912 0.572 1.00 0.00 N
ATOM 1530 HD1 HIS A 100 1.147 -3.032 -0.314 1.00 0.00 H
ATOM 1531 CG HIS A 100 2.423 -3.784 1.186 1.00 0.00 C
ATOM 1532 CE1 HIS A 100 1.331 -1.880 1.367 1.00 0.00 C
ATOM 1533 HE1 HIS A 100 0.689 -1.039 1.150 1.00 0.00 H
ATOM 1534 NE2 HIS A 100 2.032 -2.051 2.473 1.00 0.00 N
ATOM 1535 CD2 HIS A 100 2.723 -3.234 2.384 1.00 0.00 C
ATOM 1536 HD2 HIS A 100 3.385 -3.647 3.133 1.00 0.00 H
ATOM 1537 C HIS A 100 0.532 -5.916 0.474 1.00 0.00 C
ATOM 1538 O HIS A 100 -0.189 -5.279 1.241 1.00 0.00 O
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.
Xplor NIH master, could you please kindly help me solve this problem.
Thank you so much and best regards,
Zhiyu
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