disulfides and .defs, maybe custom geom.
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
Hi Bryan, Which version of phenix is this? Do you specify the .pdb file again, along with the .def file? In older versions the .pdb file was read twice. Newer versions will handle this the way you want to. In any case, it is always best to run phenix.refine some.def No need to specify the .pdb and .mtz files again, irrespective of the phenix.refine version. Ralf
participants (2)
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Bryan W. Lepore
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Ralf W. Grosse-Kunstleve