[phenixbb] pdb LINK record lost after phenix refine in GUI

Pavel Afonine 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).

Pavel

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 " 
> distance=2.04
>   Custom bonds:
>     bond:
>       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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