Hi, In answer to Nikolay's question about ESP values in various positions: 1) Elaine is absolutely right in pointing you to the APBS bb. If you look in their FAQ you'll notice that the question has been addressed several times. 2) There is an 'atompot' command that you can use when you run apbs. It'll print the values for each atom in the pdb, the only problem is that last time I tried it there were no atom names in output which was difficult for me (apbs team were supposed to add that feature) but x,y.z were there. 3) If atompot is not what you need somebody in the abps team will surely help you. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] on behalf of chimera-users-request@cgl.ucsf.edu [chimera-users-request@cgl.ucsf.edu] Sent: Thursday, May 24, 2012 10:00 PM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 109, Issue 28 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Fwd: ESP calculations (Eric Pettersen) 2. APBS output format (Elaine Meng) 3. Hydrogen bond energy calculation (Aditya Padhi) 4. Re: Hydrogen bond energy calculation (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 23 May 2012 13:18:14 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Subject: [Chimera-users] Fwd: ESP calculations Message-ID: <4C557064-D2EC-45A5-9523-B35E683C76D5@cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii"; Format="flowed"; DelSp="yes" Begin forwarded message:
From: Nikolay Igorovich Rodionov <nirodion@syr.edu> Date: May 21, 2012 12:43:34 PM PDT To: Eric Pettersen <pett@cgl.ucsf.edu> Subject: RE: [Chimera-users] ESP calculations
Thank you both,
Can either of you tell me how the information in a volume data set is organized? I am looking at a .dx file that I created using APBS which I would assume to be very similar to the volumetric data sets created by Chimera. What does each column of data represent? Is there any way for me to sort the ESP data based on position using Excel or Matlab? I am only concerned with ESP data for one region of molecule. If you could point me in the direction of some good documentation on this file type it would be great.
I don't know, so I'm forwarding this out to chimera-users land, where someone might have an answer... --Eric
Thanks again, Nikolay Rodionov
-----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Monday, May 21, 2012 2:57 PM To: chimera-users@cgl.ucsf.edu BB Cc: Nikolay Igorovich Rodionov Subject: Re: [Chimera-users] ESP calculations
Also, if you compute a volume, you can use the "Values at Atom Positions" tool to, um, get the values at atom positions (say, a ligand), if that's relevant to what you're doing.
--Eric
On May 21, 2012, at 9:09 AM, Elaine Meng wrote:
Hi Nikolay, You can generate a grid of values with the "Compute grid" option of Coulombic Surface Coloring (or corresponding option of the "coulombic" command). The grid is a volume data set, and when it is generated the Volume Viewer and Surface Color dialogs will automatically appear.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/ co ulombic.html
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/ co ulombic.html#volume
You can save the grid to a file with the FIle menu of Volume Viewer. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ volumeviewer /framevolumeviewer.html
As for the values at each point of the surface, I don't know of a way to write these all to a file, but in Surface Color if you click the Options button and then turn on the option to "Report value at mouse position" it will report the values in the status line at the bottom of the Chimera window when you click into the graphics window and then mouse over the surface. I just noticed that to make this work it is necessary to recolor the surface first by clicking the Color button on this dialog, which may be a bug, but that's the workaround! <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ su rfcolor.html
If you have the grid file saved you can reopen it in Chimera later and use it in Surface Color without rerunning the ESP calculation.
However, keep in mind that Coulombic ESP is more for qualitative purposes of visualization or making comparisons between related structures than for absolute quantitative accuracy. For example, you could easily make all the ESP values half as large simply by doubling the dielectric constant used in their calculation, as shown in the equation in the Coulombic Surface Coloring manual page.
I hope this helps, 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 May 21, 2012, at 8:05 AM, Nikolay Igorovich Rodionov wrote:
Hi all, I was wondering if there was a way to get an output data file regarding ESP coloring and calculations based on Coulomb's law. The visualization is great but I would also like to quantify the data. Thank you, Nikolay Rodionov
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