Re: [PyMOL] Clip surface only

Thanks to both of you, guys.

I settled on something far more trivial, sparked by the hide everything command in Tsjerk’s suggestion ☺  Involves a tiny bit of manual labor but works for me.

Cheers and Thanks!
Markus

From: Tsjerk Wassenaar [mailto:ts...@gm...]
Sent: Wednesday, January 21, 2015 1:49 PM
To: H. Adam Steinberg
Cc: Markus Heller; pym...@li...
Subject: Re: [PyMOL] Clip surface only


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.a...@gm...<mailto:h.a...@gm...>> 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 <mh...@cd...<mailto:mh...@cd...>> 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
>
>
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