Hey :)
If you want to do it using only Pymol in just a few minutes, try this:
set auto_zoom, 0
scale=1.0
import numpy
M=numpy.array(cmd.get_view()).reshape(6,3)
cmd.pseudoatom("dummy",pos=list(M[4,:]-scale*numpy.dot(M[:3,:3],M[3,:])))
hide everything, (not ligand) within 150 of dummy
Adjust the scale to get a more curved or more planar clip.
Hope it helps,
Tsjerk
On Wed, Jan 21, 2015 at 10:21 PM, H. Adam Steinberg <
h.adam.steinb...@gmail.com> wrote:
> if you have access to Gimp or photoshop and want to do this in just a few
> minutes… clip and render the surface how you want it, then without moving
> anything, unclip and render just the ligand. In any bitmap editing program
> layer the ligand image over the clipped surface image and merge the two
> into one image.
>
>
> > On Jan 21, 2015, at 2:57 PM, Markus Heller <mhel...@cdrd.ca> wrote:
> >
> > Hello all,
> >
> > I'm trying to show a ligand in a binding site, and I'd like to
> selectively clip the surface only. I haven't found anything on the web,
> only that it was not possible a few years ago.
> >
> > Surely this has changed?
> >
> > Thanks and Cheers
> > Markus
> >
> >
> > --
> > Markus Heller, Ph.D.
> > NMR Scientist
> > CDRD - The Centre for Drug Research and Development
> > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604)
> 827-1147
> > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca |
> www.cdrd.ca
> >
> >
> >
> >
> >
> >
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--
Tsjerk A. Wassenaar, Ph.D.
------------------------------------------------------------------------------
New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
Higher redundancy.Lower latency.Increased capacity.Completely compliant.
http://p.sf.net/sfu/gigenet
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