[Chimera-users] Electric field lines?

Francois¡¡Charles Matthieu¡¡Berenger Berenger at riken.jp
Wed Dec 12 18:06:17 PST 2012


There is an APBS plugin in pymol,
you can see the field lines once the calculation
is finished (if it managed to run APBS, sometimes it crashes
depending on the input PDB).

On Wed, 12 Dec 2012 15:46:38 -0500
"Hurt, Darrell (NIH/NIAID) [E]" <darrellh at niaid.nih.gov> wrote:

> Hi Elaine!
> 
> OK. I see what you've done with this picture and I think I can reproduce it. I think it will work for my purposes.
> 
> What I was hoping for is illustrated in various ways on the following pages. Maybe it is something to be included in future Chimera releases...
> 
> http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-vmd
> http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/images/fieldlines.jpg
> http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Electric_Field_Lines
> 
> Thanks for your awesome work and endless creativity!
> Darrell
> 
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> 
> Office  301-402-0095
> Mobile 301-758-3559
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> 
> Disclaimer: The information in this e-mail and any of its attachments is 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. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: Wednesday, December 12, 2012 03:33 PM
> To: Hurt, Darrell (NIH/NIAID) [E]
> Cc: chimera-users at cgl.ucsf.edu List <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Electric field lines?
> 
> Hi Darrell!
> You could show isosurfaces at multiple levels but for only a single plane of the data... essentially contour lines.  There is a very brief mention of that in the "Planes" section of the Volume Viewer page:
> 
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#planes>
> 
> It is somewhat labor-intensive if you want to show a lot of levels, I admit.
> 
> Example image below.  I had also displayed the molecular surface and per-model-clipped it in almost the same plane as the contour lines, but that is an independent part of the setup.  I can send the session to you if that would help.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> [cid:fba60b94-6284-4310-9a29-80159a0daf2e at mail.nih.gov]
> 
> On Dec 12, 2012, at 12:08 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:
> 
> > Hi Chimera team,
> >
> > Is it possible to visualize electric field lines in Chimera from, for example, an APBS run? If so, how do I do it? I've scanned through the documentation, but didn't find anything…
> >
> > Thanks,
> > Darrell
> >
> >
> > Darrell Hurt, Ph.D.
> > Section Head, Computational Biology
> > Bioinformatics and Computational Biosciences Branch (BCBB)
> > OCICB/OSMO/OD/NIAID/NIH
> >
> > 31 Center Drive, Room 3B62B, MSC 2135
> > Bethesda, MD 20892-2135
> > Office  301-402-0095
> > Mobile 301-758-3559
> > http://bioinformatics.niaid.nih.gov (Within NIH)
> > http://exon.niaid.nih.gov (Public)
> >
> > Disclaimer: The information in this e-mail and any of its attachments is 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. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> >
> > _______________________________________________
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> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
> 





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