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Hi Soca,<br>
<br>
So the problem was the APBS potential file (.dx) was computed with a
PDB that was not aligned to the PDB you were using for displaying
the potential. Glad you figured it out.<br>
<br>
Tom<br>
<br>
<br>
<blockquote type="cite">Hi Tom,
<div><br>
</div>
<div>Thanks for your quick response. I believe I have figured out
the problem. I followed your suggestion and manipulated the
volume Viewer. As I did so, at first nothing happened...however,
just changing views, I zoomed out and found a volume mass non
alined with the molecule to which I hoped to show potential.
(Please see attached image)</div>
<div><br>
</div>
<div>I found out what my problem was however. As I generated my
.pqr file (PDB2PQR) for the .dx APBS, I failed to realize that
the model (PDB) I had used for file generation had
different coordinates that the model I was visualizing, since I
had lined these molecules away from their original coordinates.
Once I figured that out, I was able to align everything
corrected and generate the electrostatic potential surface map. </div>
<div><br>
</div>
<div>I figured the issue was something trivial.</div>
<div><br>
</div>
<div>Thanks for your help nonetheless. </div>
<div><br>
</div>
<div>Soca </div>
<div><br>
<div class="gmail_quote">On Mon, Mar 26, 2012 at 2:46 PM, Tom
Goddard <span dir="ltr"></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Soca,<br>
<br>
Sounds like you are doing everything right. That makes me
suspect that something is wrong with your APBS file -- like
all the potential values are zero. To see what the
distribution of the potential values are, open the APBS file
and then use menu Tools / Volume Data / Volume Viewer, and
click on the histogram (empty rectangle in the middle of the
volume dialog). That will show a histogram of the potential
values. You can move the vertical bar on the histogram to
see what the potential value is at that position. Check if
-5 to 5 is a reasonable range.<span class="HOEnZb"><font
color="#888888"><br>
<br>
Tom</font></span>
<div class="HOEnZb">
<div class="h5"><br>
<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<br>
<br>
I have been attempting to generate a electrostatic
surface map in chimera using an external potential
file generated from APBS (.dx).<br>
<br>
I understand that Chimera has an internal surface
calculation protocol via Coulombic Surface Coloring,
however, I would like to use the Electrostatic Surface
Coloring.<br>
<br>
However, when I open my molecule (PDB), show surfaces,
and choose its MSMS main surface to color by
electrostatic potential using the .dx file, the
surface map is not the red, white, blue that I have
set in my parameterts under Surface color. Everything
turns to grey. My other parameters include:<br>
<br>
red -5, white 0, blue 5. Colors 3. Palette Red-Blue.
Surface offset 1.4.<br>
<br>
I feel as though I am missing something trivia that
would allow me to generate the surface image I want,
however I am lost after may searches for advice
through the forums and tutorials.<br>
<br>
Please let me know what I am missing.<br>
<br>
Thanks<br>
<br>
Soca<br>
<br>
-- <br>
Ardian Soca Wibowo, Ph.D.<br>
Postdoctoral Associate<br>
Dann Research Group<br>
Department of Chemistry<br>
Indiana University<br>
</blockquote>
<br>
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</blockquote>
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</blockquote>
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