[phenixbb] disulfides and .defs, maybe custom geom.
Bryan W. Lepore
bryan.lepore at umassmed.edu
Sun Jun 8 17:53:13 PDT 2008
i can start phenix with new .pdb/.mtz, and custom geometry with
satisfactory output. problem is, when i provide that output .def file
(possibly w/ custom geometry in it) on the command line, phenix always
sets up disulfides when it didn't before:
Number of disulfides: simple=4, symmetry=0
Simple disulfide: " SG CYS A 14 " - " SG CYS A 14 " distance=0.10
Simple disulfide: " SG CYS A 140 " - " SG CYS A 140 " distance=0.08
Simple disulfide: " SG CYS A 144 " - " SG CYS A 144 " distance=0.54
Simple disulfide: " SG CYS A 147 " - " SG CYS A 147 " distance=0.18
Sorry: More than one atom selected: "chain A and resname CYS and resid 140
and name SG"
Number of selected atoms: 2
my ligands are attached to the cysteines, so i suspect some trouble here
but can't see it - shouldn't be a problem, right?
if i set disulfide_distance_cutoff= 1.0 or less, phenix drives the system
any pointers, appreciated.
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