[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>
>
>
>
>
>
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