Leave it to the crystallographers to be the last on the Planet with
text-only email readers.... Just before the ccp4bb will migrate to
google+ :)
Flip
Op 7/6/2011 10:27, Tim Gruene schreef:
> Dear Boaz (and others)
>
> it immensly improves readability of your emails if you can ask your email client
> to also include a plain text version of your email on top of the html-version
> ;-)
>
> Cheers,
>
> Tim
>
> On Tue, Jul 05, 2011 at 05:55:28PM +0000, Boaz Shaanan wrote:
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>> <div style="direction: ltr;font-family: Arial;color: #0000FF;font-size: 10pt;">Hi,
>> <div><br>
>> </div>
>> <div>The best place to pose this question would be the APBS bb which you can join from this site:</div>
>> <div><br>
>> </div>
>> <div><a href="http://www.poissonboltzmann.org/apbs/">http://www.poissonboltzmann.org/apbs/</a><br>
>> <div><br>
>> <div style="font-family:Tahoma; font-size:13px">
>> <div>You may also check the FAQ there, maybe your question (+ an answer) would be there already.</div>
>> <div><br>
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>> <div><font face="Times New Roman" size="3"></font> Cheers,</div>
>> <div><br>
>> </div>
>> <div> Boaz</div>
>> <div><font face="Times New Roman" size="3"></font> </div>
>> <div><font color="#000080" face="Times New Roman" size="3"><em>Boaz Shaanan, Ph.D.
>> <br>
>> Dept. of Life Sciences <br>
>> Ben-Gurion University of the Negev <br>
>> Beer-Sheva 84105 <br>
>> Israel <br>
>> <br>
>> E-mail: [log in to unmask]<br>
>> Phone: 972-8-647-2220 Skype: boaz.shaanan <br>
>> Fax: 972-8-647-2992 or 972-8-646-1710 </em></font></div>
>> <div><font color="#000080" face="Times New Roman" size="3"><em></em></font> </div>
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>> <div id="divRpF112756" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> CCP4 bulletin board [[log in to unmask]] on behalf of Reginald McNulty [[log in to unmask]]<br>
>> <b>Sent:</b> Tuesday, July 05, 2011 8:24 PM<br>
>> <b>To:</b> [log in to unmask]<br>
>> <b>Subject:</b> [ccp4bb] APBS<br>
>> </font><br>
>> </div>
>> <div></div>
>> <div>
>> <div>Dear CCP4BB,</div>
>> <div><br>
>> </div>
>> <div>I apologize for the off topic question.</div>
>> <div><br>
>> </div>
>> <div>I have determined the 3D structure of a membrane protein transporter and want to make a figure showing the surface charge. So, I ran PDB2PQR and specified pH 5.4. I understand the next step is to run APBS. I know there are different dielectric constants
>> for parts of the protein exposed to membrane and cytosolic portions. I'm wondering if I need to take this into account when generating a figure for surface charge? If so, I'm wondering how do I tell the program residues that are embedded in the membrane
>> and those that are not?</div>
>> <div><br>
>> </div>
>> <div>If you could help me answer these questions or point me in the right direction I'd greatly appreciate it.</div>
>> <div><br>
>> </div>
>> <div>Best regards,</div>
>> <div><br>
>> </div>
>> <div>Reggie McNulty</div>
>> <div>Department of Molecular Biology and Biochemistry</div>
>> <div>UC Irvine</div>
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