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

[Chen Chen]

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