<div dir="ltr">Dear All,<div><br></div><div>Thank you so much for your suggestion.</div><div><br></div><div>Best Regards,</div><div>Sunisa Yoodee</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">ในวันที่ จ. 21 ก.พ. 2022 เวลา 01:00 Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> เขียนว่า:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Sunisa,<br>
There is no single value for a protein - the electrostatic potential is a quantity that varies in 3D space, so instead of one value it is many different values on a 3D grid.<br>
<br>
Getting to Jacob's question of how to save values:<br>
<br>
ChimeraX does not yet have the option to generate a map model from the Coulombic electrostatic potential calculation.  To do that, you would need to use Chimera instead.  Chimera's "coulombic" command, see the last 3 options on this page:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html</a>><br>
<br>
... or the GUI, Chimera menu: Tools... Structure Analysis.... Coulombic Surface Coloring, the "Compute grid..." options:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html</a>><br>
<br>
Then in Chimera, you could save that map model to a file with the "volume" command, see saving options:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output</a>><br>
<br>
Formats are MRC, NetCDF, BRIX, IMAGIC, or Chimera map format.  I don't know if they are meant to be  human-readable, you would need to investigate that further yourself.<br>
<br>
Alternatively if you just mean you want to know the value of the potential at some specific point(s) on the protein surface, see this recent post:<br>
<<a href="https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003337.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003337.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.                       <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Feb 19, 2022, at 6:05 AM, Anderson, Jacob via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> To piggy back on this question of getting more quantitative information out of ChimeraX's electrostatic/coloumbic functions, is there a way to save information about the electrostatic surface as a readable text file (or a .dx file (if that one is human readable))?  I was hoping to quantitatively get a delta electrostatic surface of two surfaces at different propka-ph values. <br>
> <br>
> Or perhaps a way to generate that difference surface in ChimeraX?<br>
> From: ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" target="_blank">chimerax-users-bounces@cgl.ucsf.edu</a>> on behalf of Sunisa Yoodee via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br>
> Sent: Saturday, February 19, 2022 12:22 AM<br>
> To: <a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a> <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br>
> Subject: [chimerax-users] Question about Coulombic electrostatic potential<br>
>  <br>
> Dear UCSF ChimeraX<br>
> <br>
> We used the ChimeraX program to calculate electrostatic potential. By using the coulombic command, a molecular surface was generated and colored. However, we also need the electrostatic potential value (kcal/(mol*e))of the protein. Could you please give some advices how to get this value?<br>
> <br>
> Best Regards,<br>
> Sunisa Yoodee<br>
> -- <br>
> Sunisa Yoodee, Ph.D<br>
> <br>
> Medical Proteomics Unit, <br>
> Faculty of Medicine Siriraj Hospital, <br>
> Mahidol University,<br>
> 6th Floor SiMR Building,<br>
> 2 Wanglang Road, Bangkoknoi,<br>
> Bangkok 10700, THAILAND<br>
> Tel: 66-8-06691102<br>
> e-mail: <a href="mailto:yd.sunisa@gmail.com" target="_blank">yd.sunisa@gmail.com</a><br>
> <br>
> <br>
> _______________________________________________<br>
> ChimeraX-users mailing list<br>
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<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><font size="2"><span style="font-family:arial,helvetica,sans-serif"><b>Sunisa Yoodee</b>, Ph.D<br></span></font><div><font size="2"><span style="font-family:arial,helvetica,sans-serif"><br></span></font></div><font size="2"><span style="font-family:arial,helvetica,sans-serif"><span>
</span>
</span></font><div><font size="2"><span style="font-family:arial,helvetica,sans-serif"><span style="background-color:rgb(255,255,255)">Medical Proteomics Unit, </span></span></font></div><font size="2"><span style="font-family:arial,helvetica,sans-serif">
<span></span><span></span><span></span>
</span></font><div><font size="2"><span style="font-family:arial,helvetica,sans-serif"><span style="background-color:rgb(255,255,255)">Faculty of Medicine Siriraj Hospital, </span></span></font></div><font size="2"><span style="font-family:arial,helvetica,sans-serif">
<span></span><span></span><span></span>
</span></font><div><font size="2"><span style="font-family:arial,helvetica,sans-serif"><span style="background-color:rgb(255,255,255)">Mahidol University,</span></span></font></div><font size="2"><span style="font-family:arial,helvetica,sans-serif">
<span></span><span></span><span></span>
</span></font><div><font size="2"><span style="font-family:arial,helvetica,sans-serif"><span style="background-color:rgb(255,255,255)">6th Floor SiMR Building,</span></span></font></div><font size="2"><span style="font-family:arial,helvetica,sans-serif">
<span></span><span></span><span></span>
</span></font><div><font size="2"><span style="font-family:arial,helvetica,sans-serif"><span style="background-color:rgb(255,255,255)">2 Wanglang Road, Bangkoknoi,</span></span></font></div><font size="2"><span style="font-family:arial,helvetica,sans-serif">
<span></span><span></span><span></span>
</span></font><div><font size="2"><span style="font-family:arial,helvetica,sans-serif"><span style="background-color:rgb(255,255,255)">Bangkok 10700, THAILAND</span></span></font></div><font size="2"><span style="font-family:arial,helvetica,sans-serif">
<span></span><span></span><span></span>
</span></font><div><font size="2"><span style="font-family:arial,helvetica,sans-serif">Tel: 66-8-06691102<br>e-mail: <a href="mailto:yd.sunisa@gmail.com" style="color:rgb(17,85,204)" target="_blank">yd.sunisa@gmail.com</a></span></font><br><div><br></div><div><br></div></div></div></div></div></div></div></div></div></div></div></div>