Electric field lines?
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.
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 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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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-electrostat... http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/images/fieldlines.jpg http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Electri... 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 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. From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Wednesday, December 12, 2012 03:33 PM To: Hurt, Darrell (NIH/NIAID) [E] Cc: chimera-users@cgl.ucsf.edu List <chimera-users@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@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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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-electrostat... http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/images/fieldlines.jpg http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Electri...
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 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.
From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Wednesday, December 12, 2012 03:33 PM To: Hurt, Darrell (NIH/NIAID) [E] Cc: chimera-users@cgl.ucsf.edu List <chimera-users@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@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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Darrell, I made a Python Chimera script to show electrostatic field lines using a potential map. I've attached an example picture. Didn't have time today to put this into the Chimera daily build. Tom On Dec 12, 2012, at 12:08 PM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@niaid.nih.gov> 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
Hi Tom, This is fantastic! I noticed that you've even colored the lines by their potential. Excellent! Thank you. I look forward to using it soon! 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. From: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> Date: Thursday, December 13, 2012 1:10 AM To: Darrell Hurt <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> List" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Electric field lines? Hi Darrell, I made a Python Chimera script to show electrostatic field lines using a potential map. I've attached an example picture. Didn't have time today to put this into the Chimera daily build. Tom [cid:AC7D498F-1D49-49C8-9E7E-91C336C2F0D0] On Dec 12, 2012, at 12:08 PM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> 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
Hi Darrell, Ok I checked in the electrostatic field line code. It will be in tonight's Chimera daily build but not in the Chimera 1.7 release candidate. The code is slow (10 seconds for 1000 lines of a 100**3 potential map) and I'd like to make some other improvements, but I put it in as is so you can try it right away if you like. Here's an example, open potential.dx measure fieldLines #0 lines 500 startAbove 10 color pink linewidth 2 scolor #1 volume #0 cmap -10,red:0,white:10,blue The measure command creates the lines and the scolor command colors them. The lines parameter is how many lines to show, with lines starting at potential magnitudes above 10 (startAbove). There is some trickiness to which field lines are shown that is described in the email below to Conrad. Tom
On 12/13/2012 9:48 AM, Tom Goddard wrote:
Hi Conrad,
Good question. This is the whole problem with showing field lines -- which of the infinity of lines to show. I think a main impression of the lines is given by how dense they are in different regions. That just depends on which you choose to show. So the answer is I tried something crazy and in that image. The idea was I'd like lines to originate around charges and the number of lines around a charge to be proportional to the charge. I want to do it with only the map. So I compute the magnitude of the gradient squared divided by the potential at every grid point and use the grid points with the largest N values for starting N field lines. Here's my rather shaky reasoning. Near a point charge the potential is q/r. The gradient squared divided by the potential is q/r**3 ( = (q/r**2)**2 / (q/r) ). If the chosen points have grad squared / potential > C then they are grid points where q/r**3 > C, in other words r**3 < q/C. The number of grid points around a charge used is proportional to the volume r**3 so is linear in charge. That's the theory. I realized this morning the APBS potential probably uses a Gaussian charge distribution for each charge (it uses atom radius I think). So the potential close to the charge is not q/r -- no singularity at the charge position. But it still seems to concentrate field lines around charges and more around bigger charges. Probably there are better approaches and probably different field line choosing methods would be handy depending on what one wants to show. It's a can of worms.
Tom
On Dec 13, 2012, at 9:31 AM, Conrad Huang wrote:
Just out of curiosity, how are the field lines chosen? There are obviously many lines to choose from, but your image shows lines that almost look hand selected. Good job!
Conrad
On Dec 13, 2012, at 5:37 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote:
Hi Tom,
This is fantastic! I noticed that you've even colored the lines by their potential. Excellent!
Thank you. I look forward to using it soon!
Darrell
Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
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: Tom Goddard Date: Thursday, December 13, 2012 1:10 AM To: Darrell Hurt Cc: chimera-users Subject: Re: [Chimera-users] Electric field lines?
Hi Darrell,
I made a Python Chimera script to show electrostatic field lines using a potential map. I've attached an example picture. Didn't have time today to put this into the Chimera daily build.
Tom
[cid:AC7D498F-1D49-49C8-9E7E-91C336C2F0D0]
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
<fieldlines_2sod.jpg>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Elaine Meng -
Francois¡¡Charles Matthieu¡¡Berenger -
Hurt, Darrell (NIH/NIAID) [E] -
Tom Goddard