 |
 |
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: >> <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> >>