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The APBS electrostatic potential grid file format (suffix .dx) is
from IBM's Visualization Data Explorer and also used by an open
source program based on that software called OpenDX. It is
documented in the APBS manual here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data">http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data</a><br>
<br>
Tom<br>
<br>
<blockquote
cite="mid:4C557064-D2EC-45A5-9523-B35E683C76D5@cgl.ucsf.edu"
type="cite">
<div>
<div>Begin forwarded message:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; "><font style="font:
16.0px Helvetica; color: #000000" face="Helvetica"
color="#000000" size="5"><b>From: </b></font><font
style="font: 16.0px Helvetica" face="Helvetica" size="5">Nikolay
Igorovich Rodionov <br>
</font></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; "><font style="font:
16.0px Helvetica; color: #000000" face="Helvetica"
color="#000000" size="5"><b>Date: </b></font><font
style="font: 16.0px Helvetica" face="Helvetica" size="5">May
21, 2012 12:43:34 PM PDT</font></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; "><font style="font:
16.0px Helvetica; color: #000000" face="Helvetica"
color="#000000" size="5"><b>To: </b></font><font
style="font: 16.0px Helvetica" face="Helvetica" size="5">Eric
Pettersen <br>
</font></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; "><font style="font:
16.0px Helvetica; color: #000000" face="Helvetica"
color="#000000" size="5"><b>Subject: </b></font><font
style="font: 16.0px Helvetica" face="Helvetica" size="5"><b>RE:
[Chimera-users] ESP calculations</b></font></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br>
</div>
</div>
<div>Thank you both,<br>
<br>
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.<br>
</div>
</blockquote>
<div><br>
</div>
I don't know, so I'm forwarding this out to chimera-users land,
where someone might have an answer...</div>
<div><br>
</div>
<div>--Eric</div>
<div><br>
<blockquote type="cite">
<div><br>
Thanks again,<br>
Nikolay Rodionov<br>
<br>
-----Original Message-----<br>
From: Eric Pettersen <br>
Sent: Monday, May 21, 2012 2:57 PM<br>
To: <a moz-do-not-send="true"
href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>
BB<br>
Cc: Nikolay Igorovich Rodionov<br>
Subject: Re: [Chimera-users] ESP calculations<br>
<br>
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.<br>
<br>
--Eric<br>
<br>
On May 21, 2012, at 9:09 AM, Elaine Meng wrote:<br>
<br>
<blockquote type="cite">Hi Nikolay,<br>
</blockquote>
<blockquote type="cite">You can generate a grid of values
with the "Compute grid" option of <br>
</blockquote>
<blockquote type="cite">Coulombic Surface Coloring (or
corresponding option of the "coulombic" <br>
</blockquote>
<blockquote type="cite">command). The grid is a volume data
set, and when it is generated the <br>
</blockquote>
<blockquote type="cite">Volume Viewer and Surface Color
dialogs will automatically appear.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/co">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/co</a><br>
</blockquote>
<blockquote type="cite">ulombic.html<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite"><<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/co">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/co</a><br>
</blockquote>
<blockquote type="cite">ulombic.html#volume<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">You can save the grid to a file with
the FIle menu of Volume Viewer.<br>
</blockquote>
<blockquote type="cite"><<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer</a><br>
</blockquote>
<blockquote type="cite">/framevolumeviewer.html<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">As for the values at each point of
the surface, I don't know of a way <br>
</blockquote>
<blockquote type="cite">to write these all to a file, but in
Surface Color if you click the <br>
</blockquote>
<blockquote type="cite">Options button and then turn on the
option to "Report value at mouse <br>
</blockquote>
<blockquote type="cite">position" it will report the values
in the status line at the bottom <br>
</blockquote>
<blockquote type="cite">of the Chimera window when you click
into the graphics window and then <br>
</blockquote>
<blockquote type="cite">mouse over the surface. I just
noticed that to make this work it is <br>
</blockquote>
<blockquote type="cite">necessary to recolor the surface
first by clicking the Color button on <br>
</blockquote>
<blockquote type="cite">this dialog, which may be a bug, but
that's the workaround!<br>
</blockquote>
<blockquote type="cite"><<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/su">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/su</a><br>
</blockquote>
<blockquote type="cite">rfcolor.html<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">If you have the grid file saved you
can reopen it in Chimera later and <br>
</blockquote>
<blockquote type="cite">use it in Surface Color without
rerunning the ESP calculation.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">However, keep in mind that Coulombic
ESP is more for qualitative <br>
</blockquote>
<blockquote type="cite">purposes of visualization or making
comparisons between related <br>
</blockquote>
<blockquote type="cite">structures than for absolute
quantitative accuracy. For example, you <br>
</blockquote>
<blockquote type="cite">could easily make all the ESP values
half as large simply by doubling <br>
</blockquote>
<blockquote type="cite">the dielectric constant used in
their calculation, as shown in the <br>
</blockquote>
<blockquote type="cite">equation in the Coulombic Surface
Coloring manual page.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">I hope this helps,<br>
</blockquote>
<blockquote type="cite">Elaine<br>
</blockquote>
<blockquote type="cite">----------<br>
</blockquote>
<blockquote type="cite">Elaine C. Meng, Ph.D.<br>
</blockquote>
<blockquote type="cite">UCSF Computer Graphics Lab (Chimera
team) and Babbitt Lab Department <br>
</blockquote>
<blockquote type="cite">of Pharmaceutical Chemistry
University of California, San Francisco<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">On May 21, 2012, at 8:05 AM, Nikolay
Igorovich Rodionov wrote:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Hi all,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">I was wondering if there was a way
to get an output data file <br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">regarding ESP coloring and
calculations based on Coulomb's law. The <br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">visualization is great but I would
also like to quantify the data.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Thank you,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Nikolay Rodionov<br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">_______________________________________________<br>
</blockquote>
<blockquote type="cite">Chimera-users mailing list<br>
</blockquote>
<blockquote type="cite"><a moz-do-not-send="true"
href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>
</blockquote>
<blockquote type="cite"><a moz-do-not-send="true"
href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<br>
<br>
<br>
<br>
</div>
</blockquote>
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<br>
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