 |
 |
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: > <html dir="ltr"> > <head> > <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-8-i"> > <style type="text/css" id="owaParaStyle"></style> > </head> > <body style="word-wrap:break-word" fpstyle="1" ocsi="0"> > <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> > </div> > <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> > <div><font color="#000080" face="Times New Roman" size="3"><em></em></font> </div> > <div><font face="Times New Roman" size="3"><em><font color="#000080"> > <br> > <br> > </font></em></font></div> > <font face="Times New Roman" size="3"></font></div> > </div> > <div style="font-family: Times New Roman; color: #000000; font-size: 16px"> > <hr tabindex="-1"> > <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> > <div><span class="Apple-style-span" style="color: rgb(0, 0, 255); "><br> > </span><span class="Apple-style-span" style="color: rgb(0, 0, 255); "></span></div> > <div><span class="Apple-style-span" style="color:rgb(0,0,255); font-family:'Times New Roman'; font-size:16px"> </span></div> > <div><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-align:auto; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px; font-size:medium"><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-size:medium; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px"> > <div style="word-wrap:break-word"> > <div> > <div style="margin-top:0in; margin-right:0in; margin-bottom:0.0001pt; margin-left:0in"> > <font class="Apple-style-span" color="#0000FF" face="'Times New Roman'" size="4"><span class="Apple-style-span" style="font-size:16px"><br> > </span></font></div> > <div style="margin-top:0in; margin-right:0in; margin-bottom:0.0001pt; margin-left:0in"> > <font class="Apple-style-span" color="#0000FF" face="'Times New Roman'" size="4"><span class="Apple-style-span" style="font-size:16px"><br> > </span></font></div> > <div style="margin-top:0in; margin-right:0in; margin-bottom:0.0001pt; margin-left:0in"> > <font class="Apple-style-span" color="#0000FF" face="'Times New Roman'" size="4"><span class="Apple-style-span" style="font-size:16px"><br> > </span></font></div> > </div> > </div> > </span></span></div> > <br> > </div> > </div> > </div> > </div> > </body> > </html> > -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A