Re: [PyMOL] wire-mesh spheres?

Matthew Baumgartner Wed, 24 Oct 2012 14:09:46 -0700

Hi,

So some brief background, I am writing a pymol plugin for displayingpharmacophores queries from ZincPharmer (http://zincpharmer.csb.pitt.edu/), which is developed in my lab. Version1 of my plugin is available here:http://sourceforge.net/projects/pharmer/files/ under the name load_query.

Sorry if that quickly turned into an advertisement, but what I wouldlike to be able to reproduce in pymol is something like this:http://i.imgur.com/hiX2i.png . Where the wire mesh sphere's representthe pharamacophores. Currently, I am using the cgo sphere's but they donot do well when there are overlapping pharmacophores (a common case).




Thanks,
Matt

On 10/24/2012 03:06 PM, Jason Vertrees wrote:

Hi Matt,

There's currently no easy way to do this. Can you please send us some
screenshots of what you'd like to see implemented?

Cheers,

-- Jason

On Tue, Oct 23, 2012 at 4:16 PM, Matthew Baumgartner <mp...@pitt.edu> wrote:

Hi,
Is it now possible to have wire mesh cgo object spheres in pymol?
I found this thread from a while ago (2004) but googleing, I didn't
find anything more recent.


The one sort of work around that I though of was to create pseudo-atoms
and somehow modify their radius and then show them as mesh.
But I would like to use CGO objects if possible.

Does anyone have any suggestions?

Thanks,
Matt Baumgartner



Sphere transparency example included below...

ALPHA must preceed COLOR to be effective.

PyMOL does not yet do a global sort of tranparent triangles, so there will
be artifacts in OpenGL.  Raytracing should look fine however.

# from within a .py OR .pym file...

from pymol.cgo import *
from pymol import cmd

obj = [

    ALPHA,  1.0,
    COLOR,  1.0, 1.0, 1.0,
    SPHERE, 0.0, 0.0, 0.0, 0.5,

    ALPHA,  0.66,
    COLOR,  1.0, 0.0, 0.0,
    SPHERE, 1.0, 0.0, 0.0, 0.5,

    ALPHA,  0.33,
    COLOR,  0.0, 1.0, 0.0,
    SPHERE, 0.0, 1.0, 0.0, 0.5,

    ALPHA,  0.11,
    COLOR,  0.0, 0.0, 1.0,
    SPHERE, 0.0, 0.0, 1.0, 0.5,
]

cmd.load_cgo(obj,'cgo01')

Cheers,war...@delanoscientific.com
Warren

--
Warren L. DeLano, Ph.D.
Principal Scientist

. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080
. Biz:(650)-872-0942  Tech:(650)-872-0834
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com

-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Michael George Lerner
Sent: Wednesday, November 17, 2004 9:43 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] wire-mesh spheres?


Hi,

I want to draw a bunch of spheres of various sizes and
colors.  I'm currently using cgos for this.  No problem.
Now, I also want to draw wire-mesh spheres.  Does anyone have
a script for making these?  While I'm at it, is there a way
to make cgos transparent?

Thanks,

-Michael

--
This isn't a democracy;|                        _  |Michael Lerner
   it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
-Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
                         |                       / \ | mler...@umich


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Re: [PyMOL] wire-mesh spheres?

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