[phenixbb] unexpected automatic linking between ligands in phenix.refine
Pavel Afonine
pafonine at lbl.gov
Sun Feb 5 09:13:14 PST 2017
Hi Jack,
could you please send PDB files *before* and *after* refinement and data
file (and ligand CIF file, if used)? Please make sure sending files to
me directly (not entire mailing list!).
Thanks,
Pavel
On 2/5/17 09:00, Tanner, John J. wrote:
> Dear phenix users,
>
> I’m refining a model that has FAD and SO4 ligands. Phenix makes a
> covalent bond between the N3 of the FAD and an O atom of SO4 during
> the automatic linking stage, even though the distance between the
> atoms is larger than the automatic link distance. The covalent bond
> yanks the ligands out of their density. I suppose I could disable
> automatic linking, but I’ve never seen this happen. I note that we
> recently upgraded to phenix-1.11.1-2575, and this may be my first
> refinement calculation with the new version. Output is shown below.
>
> I welcome any suggestions.
>
> Thanks,
>
> Jack
>
> -------------------------------------------------------------------------------
> PHENIX: Python-based Hierarchical ENvironment for Integrated
> Xtallography
> Version: 1.11.1
> Release tag: 2575
> Platform: intel-linux-2.6-x86_64
> User: tannerjj
> -------------------------------------------------------------------------------
>
>
> ---------------------------------------------------------------
> From the phenix.refine log file:
>
> Automatic linking
> Parameters for automatic linking
> Linking & cutoffs
> Metal : False - 3.50
> Amimo acid : False - 1.90
> Carbohydrate : True - 1.99
> Ligands : True - 1.99
> Amino acid - RNA/DNA : False
>
> Number of custom bonds: simple=2, symmetry=0
> Number of additional bonds: simple=2, symmetry=0
> Coordination:
> Other bonds:
> Simple bond: pdb=" N3 FAD C 601 "- pdb=" O2 SO4 F 605 "
> Simple bond: pdb=" N3 FAD D 601 "- pdb=" O4 SO4 F 606 "
> Time building additional restraints: 2.29
> Conformation dependent library (CDL) restraints added in 636.6
> milliseconds
> .
> .
> .
>
> Bond restraints: 15971
> Sorted by residual:
> bond pdb=" N3 FAD D 601 "
> pdb=" O4 SO4 F 606 "
> ideal model delta sigma weight residual
> 1.297 3.084 -1.787 1.00e-02 1.00e+04 3.19e+04
> bond pdb=" N3 FAD C 601 "
> pdb=" O2 SO4 F 605 "
> ideal model delta sigma weight residual
> 1.297 2.975 -1.678 1.00e-02 1.00e+04 2.81e+04
>
> ---------------------------------------------------------------
>
> The output refined PDB file shows the links were made. The LINK lines
> were not in the input PDB file.
>
> LINK N3 FAD C 601 O2 SO4 F 605
> LINK N3 FAD D 601 O4 SO4 F 606
>
> ---------------------------------------------------------------
>
>
> John J. Tanner, PhD
> Professor of Biochemistry and Chemistry
> Director, Biochemistry Graduate Admissions Committee
> Department of Biochemistry
> University of Missouri-Columbia
> 117 Schweitzer Hall
> 503 S. College Avenue
> Columbia, MO 65211
> Phone: 573-884-1280
> Fax: 573-882-2754
> Email: tannerjj at missouri.edu <mailto:tannerjj at missouri.edu>
> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
> <http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html>
>
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170205/dd1082bd/attachment.htm>
More information about the phenixbb
mailing list