[phenixbb] how to avoid self disulfide bond in phenix refinement?

[Peter Zwart]

Hi Chen,

This is because foo.param also gives the instruction to read in a pdb file.
You are basically reading in a pdb file twice now.

try running

phenix.refine foo.param

HTH

P


2008/4/14, Chen Chen <chene at umbi.umd.edu>:
> Hi,
>  I am having a problem in phenix.refine. I ran
>  phenix.refine --dry_run foo.mtz foo.pdb
>  The program generate a parameter file named foo.param.
>  I made some modification of foo.param. Then ran
>  phenix.refine foo.mtz foo.pdb foo.param
>  The program reports a weir error message:
>  ========================== Set up restraints manager
>  ==========================
>
>   Number of disulfides: simple=3, symmetry=0
>     Simple disulfide: " SG  CYS A  29 " segID="A   " - " SG  CYS A  29 "
>  segID="A   " distance=0.00
>     Simple disulfide: " SG  CYS A 180 " segID="A   " - " SG  CYS A 180 "
>  segID="A   " distance=0.00
>     Simple disulfide: " SG  CYS A 286 " segID="A   " - " SG  CYS A 286 "
>  segID="A   " distance=0.00
>   ...
>  Sorry: Bond restraint model distance < 0.001:
>   Please inspect the output above and correct the input PDB file.
>  ========================================================================
>  It seems that the program recognized three "self-disulfide" bonds. This
>  problem happens even I do not make any modification in foo.param.
>  However, if I just ran
>  phenix.refine foo.mtz foo.pdb
>  with every parameter at default, the programs runs OK without the above
>  error.
>  I am wondering if it is a bug or if I made some mistakes.
>  Thanks
>  Chen
>
>  --
>  Chen Chen, Ph. D., Research Associate
>  Center for Advanced Research in Biotechnology (CARB),
>  University of Maryland Biotechnology Institute (UMBI),
>  9600 Gudelsky Drive, Rockville, MD 20850
>  Office Phone: 240-314-6122
>
>  _______________________________________________
>  phenixbb mailing list
>  phenixbb at phenix-online.org
>  http://www.phenix-online.org/mailman/listinfo/phenixbb
>


-- 
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
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