[Chimera-users] ESP calculations
pett at cgl.ucsf.edu
Mon May 21 11:57:23 PDT 2012
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
> "coulombic" command). The grid is a volume data set, and when it is
> generated the 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 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
> 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 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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