David,
This is a weak area for PyMOL. One thing to try is to switch to an animation
with multi-layered transparency, two_sided lighting (and other tweaks) to help
show the entire binding site volume. The approach isn't perfect, but it may
help:
fetch 1gzm, async=0
remove not a//
select my_ligand, a/ret/, enable=0
hide
show st, my_ligand
set transparency, 0.85
set transparency_mode, 1 ;# multi-layer
set two_sided_lighting
set ray_transparency_contrast, 3 ;# layer-dependent
set ray_transparency_oblique, 1.5 ;# normal-dependent
select carve_sele, my_ligand, enable=0
set surface_carve_selection, carve_sele
set surface_carve_cutoff, 4.5
set surface_quality, 1
show surface, my_ligand expand 6
zoom vis
set ray_trace_frames
set cache_frames
bg white
mset 1 x30
orient my_ligand
zoom my_ligand, 3
movie.rock
mplay
# now wait a few minutes for the movie to render and play
Cheers,
Warren
From: Margulies, David (NIH/NIAID) [E] [mailto:dmargul...@niaid.nih.gov]
Sent: Thu 5/7/2009 4:07 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Non-planar clipping?
Hi,
I would like to make a clipped illustration of a peptide-ligand binding
site, a sliced-image as it were, but because the binding site consists of
several non-linear pockets, I can't visualize all in the same clipping view.
Is there a way to make a non-planar section? Or a straightforward way of
superposing several different clipping planes with a different level of
transparency to visualize all pockets with the superposed peptide-ligand?
--
David H. Margulies, MD, PhD
Chief, Molecular Biology Section
Laboratory of Immunology, NIAID, NIH
Bldg. 10; Room 11N311
10 Center Drive
Bethesda, MD 20892-1892
email: d...@nih.gov
phone: 301-496-6429
fax: 301-496-0222
___
The information in this e-mail and any of its attachments are confidential
and may contain sensitive information. It should not be used by anyone who
is not the original intended recipient. If you have received this e-mail in
error please inform the sender and delete it from your mailbox or any other
storage devices. The National Institute of Allergy and Infectious Diseases
(NIAID) shall not accept liability for any statement made that are the
sender¹s own and not expressly made on behalf of the NIAID by one of its
representatives.
--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
