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: bshaa...@bgu.ac.il<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 [CCP4BB@JISCMAIL.AC.UK] on behalf of Reginald McNulty [rmcnu...@uci.edu]<br>
<b>Sent:</b> Tuesday, July 05, 2011 8:24 PM<br>
<b>To:</b> CCP4BB@JISCMAIL.AC.UK<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>
