[phenixbb] disulfides and .defs, maybe custom geom.

[Bryan W. Lepore]

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
   Custom bonds:
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 
into swap.

any pointers, appreciated.

-bryan