Hi Claudia,those clash visualizations are drawn by the sculpting routine, so you have to invoke sculpting in some way to get them.
This python function creates a copy of your selection, does one sculpting cycle and shows bumps for it:
from pymol import cmd
def show_bumps(selection='(all)', name='bump_check', quiet=1):
cmd.delete(name)
cmd.create(name, selection, zoom=0)
cmd.sculpt_activate(name)
cmd.show_as('cgo', name)
cmd.set('sculpt_vdw_vis_mode', 1, name)
cmd.set('sculpt_field_mask', 0x020) # cSculptVDW
strain = cmd.sculpt_iterate(name, cycles=1)
if not int(quiet):
print 'VDW Strain:', strain
return strain
cmd.extend('show_bumps', show_bumps)
Cheers,
Thomas
On 06/06/2011 01:05 PM, Claudia Scotti wrote:
Please, I have modelled several mutants of a protein with FoldX and I would like to display the clashes present in each case in PyMol. I have seen that activating the "mutate" wizard I can display clashes with red disks, but only for standard rotamers, which are not those tipically used by FoldX. Any suggestions, please? Many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Via Ferrata, 1 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673
-- Thomas Holder MPI for Developmental Biology
show_bumps.py
Description: application/chimera
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