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.create(name, selection, zoom=0)
    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)


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 Scotti
Dipartimento di Medicina Sperimentale
Sezione di Patologia Generale
Universita' di Pavia
Via Ferrata, 1
27100 Pavia
Tel. 0039 0382 986335/8/1
Facs 0039 0382 303673

Thomas Holder
MPI for Developmental Biology

Attachment: show_bumps.py
Description: application/chimera

Simplify data backup and recovery for your virtual environment with vRanger.
Installation's a snap, and flexible recovery options mean your data is safe,
secure and there when you need it. Discover what all the cheering's about.
Get your free trial download today. 
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Reply via email to