[phenixbb] how to avoid self disulfide bond in phenix refinement?
Chen Chen
chene at umbi.umd.edu
Mon Apr 14 12:08:30 PDT 2008
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
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