[phenixbb] pdb LINK record lost after phenix refine in GUI
pafonine at lbl.gov
Wed Jul 15 23:21:24 PDT 2015
All connectivity information is in .geo file: check it to see if the
bind in question is present there.
phenix.refine does not read/write LINK records given that all info is in
.geo file, and input (custom) linking is specified via custom bonds
using atom selection syntax (or clicking in the GUI).
On 7/15/15 18:04, luzuok wrote:
> Dear all,
> Although Custom geometry restrains was added (see log). After phenix
> refine, the link record was lost and there seem no bond between this
> two atoms (1.44 angstrom).
> Do you think this is a real bond? How to maintain this record?
> Any comment is appreciated!
> Best regards!
> Data resolution: 2.4
> Phenix version:v2.7
> phenix refine log:
> ======================== Summary of geometry restraints
> Number of disulfides: simple=1, symmetry=0
> Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 484 "
> Custom bonds:
> atom 1: "ATOM 1205 OG SER A 265 .*. O "
> atom 2: "HETATM 3413 C23 AIX A 700 .*. C "
> symmetry operation: x,y,z
> distance_model: 1.339
> distance_ideal: 1.330
> ideal - model: -0.009
> slack: 0.000
> delta_slack: -0.009
> sigma: 0.2000
> Total number of custom bonds: 1
> Time building geometry restraints manager: 0.20 seconds
> pdb file LINK record:
> LINK OG SER A 265 C23 AIX A 700 1555 1555
> Lu Zuokun, Ph.D. Candidate
> College of Life Science, Nankai University
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> phenixbb at phenix-online.org
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