[Chimera-users] Fwd: ESP calculations

Eric Pettersen pett at cgl.ucsf.edu
Wed May 23 13:18:14 PDT 2012

Begin forwarded message:

> From: Nikolay Igorovich Rodionov <nirodion at syr.edu>
> Date: May 21, 2012 12:43:34 PM PDT
> To: Eric Pettersen <pett at 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...


> Thanks again,
> Nikolay Rodionov
> -----Original Message-----
> From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
> Sent: Monday, May 21, 2012 2:57 PM
> To: chimera-users at 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
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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