[Chimera-users] Fwd: ESP calculations
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.
> 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
>> command). The grid is a volume data set, and when it is generated
>> Volume Viewer and Surface Color dialogs will automatically appear.
>> You can save the grid to a file with the FIle menu of Volume Viewer.
>> 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
>> 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
>> this dialog, which may be a bug, but that's the workaround!
>> If you have the grid file saved you can reopen it in Chimera later
>> 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 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
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