<html><head></head><body><div class="ydp8e4eb81dyahoo-style-wrap" style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 16px;"><div style=""><div dir="ltr" data-setdir="false" style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 16px;">Hi</div><div dir="ltr" data-setdir="false" style="">Thank you very much. Every thing is working fine but DelPhi; It isn't because I didn't wait too long. I was only doing the tutorial before I analyze my PDB 6TC5. I also used DelPhi web server. </div><div dir="ltr" data-setdir="false" style="">kindest regards,</div><div style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 16px;"><br></div><div class="ydp8e4eb81dsignature" style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 16px;"><div style="font-family:Helvetica, Arial, sans-serif;font-size:16px;"><div><div style="font-family:Helvetica, Arial, sans-serif;"><div><div style="color:rgb(0, 0, 0);font-family:Helvetica, Arial, sans-serif;font-size:16px;"><span style="font-family:monospace;">Sintayehu M. Shenkutie, Dr. rer. nat. </span></div><div dir="ltr" style="color:rgb(0, 0, 0);font-family:Helvetica, Arial, sans-serif;font-size:16px;"><span style="font-family:monospace;">Assistant Professor of Biochemistry. </span></div><div dir="ltr" style="color:rgb(0, 0, 0);font-family:Helvetica, Arial, sans-serif;font-size:16px;"><span style="font-family:monospace;">Department of Chemistry<br></span></div><div dir="ltr" style="color:rgb(0, 0, 0);font-family:Helvetica, Arial, sans-serif;font-size:16px;"><span style="font-family:monospace;">Hawassa University</span></div><div style="color:rgb(0, 0, 0);font-family:Helvetica, Arial, sans-serif;font-size:16px;"><span style="font-family:monospace;">Ethiopia</span></div><div dir="ltr" style="color:rgb(0, 0, 0);font-family:Helvetica, Arial, sans-serif;font-size:16px;"><font face="monospace">Mobile: +251902432925</font></div><div dir="ltr" style="color:rgb(0, 0, 0);font-family:Helvetica, Arial, sans-serif;font-size:16px;"><font face="monospace">Email: dr.sintayehu@hu.edu.et </font></div><div dir="ltr" style="color:rgb(0, 0, 0);font-family:Helvetica, Arial, sans-serif;font-size:16px;"><a shape="rect" href="mailto:Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de" style="color:purple;text-decoration-line:underline;" rel="nofollow" target="_blank">Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de</a></div></div><br></div></div><br></div></div></div>
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On Tuesday, December 24, 2019, 07:34:25 PM GMT+3, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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<div><div dir="ltr">Hello,<br clear="none">That sounds like a problem with your DelPhi setup, or you didn’t wait long enough for the calculation to finish. Sometimes it takes several minutes.<br clear="none"><br clear="none">Instead of DelPhi, you could try using PDB2PQR and then (on the resulting pqr file) using APBS. Chimera has interfaces to both of these:<br clear="none"><br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html</a>><br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html</a>><br clear="none"><br clear="none">…or you can use their web server directly, outside of Chimera:<br clear="none"><<a shape="rect" href="http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/" target="_blank">http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/</a>><br clear="none"><<a shape="rect" href="https://apbs-pdb2pqr.readthedocs.io/en/latest/downloads.html#web-servers" target="_blank">https://apbs-pdb2pqr.readthedocs.io/en/latest/downloads.html#web-servers</a>><br clear="none"><br clear="none">I hope this helps,<br clear="none">Elaine<br clear="none">-----<br clear="none">Elaine C. Meng, Ph.D. <br clear="none">UCSF Chimera(X) team<br clear="none">Department of Pharmaceutical Chemistry<br clear="none">University of California, San Francisco<br clear="none"><div class="yqt2304420443" id="yqtfd07287"><br clear="none">> On Dec 23, 2019, at 9:45 PM, <a shape="rect" ymailto="mailto:sintaspirulina@gmail.com" href="mailto:sintaspirulina@gmail.com">sintaspirulina@gmail.com</a> wrote:<br clear="none">> <br clear="none">> FYI<br clear="none">> I tried DelPhi for windows F95 v6 as suggested by Boaz S. but in my case the out put .phi is empty file not even truncated. <br clear="none">> regards,<br clear="none">> Sintayehu M. Shenkutie, Dr. rer. nat. <br clear="none">> Assistant Professor of Biochemistry. <br clear="none">> Department of Chemistry<br clear="none">> Hawassa University<br clear="none">> Ethiopia<br clear="none">> Mobile: +251902432925<br clear="none">> Email: <a shape="rect" ymailto="mailto:dr.sintayehu@hu.edu.et" href="mailto:dr.sintayehu@hu.edu.et">dr.sintayehu@hu.edu.et</a> <br clear="none">> <a shape="rect" ymailto="mailto:Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de" href="mailto:Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de">Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de</a><br clear="none">> <br clear="none">> On Tuesday, December 24, 2019, 08:13:52 AM GMT+3, <a shape="rect" ymailto="mailto:sintaspirulina@gmail.com" href="mailto:sintaspirulina@gmail.com">sintaspirulina@gmail.com</a> <<a shape="rect" ymailto="mailto:sintaspirulina@gmail.com" href="mailto:sintaspirulina@gmail.com">sintaspirulina@gmail.com</a>> wrote:<br clear="none">> <br clear="none">> Hello again,<br clear="none">> Thank you very much for your reply.<br clear="none">> For the bug report, my bad I might have attached the wrong file. I repeated the same thing with the .phi file. The email from another user, that is probably helpful. I will see if I can get the old DelPhi version.<br clear="none">> kindest regards,<br clear="none">> <br clear="none">> <br clear="none">> On Tuesday, December 24, 2019, 12:27:54 AM GMT+3, Elaine Meng <<a shape="rect" ymailto="mailto:meng@cgl.ucsf.edu" href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br clear="none">> <br clear="none">> <br clear="none">> In case you didn’t see it, another user says this:<br clear="none">> <br clear="none">>> Begin forwarded message:<br clear="none">>> <br clear="none">>> From: Boaz Shaanan <<a shape="rect" ymailto="mailto:bshaanan@bgu.ac.il" href="mailto:bshaanan@bgu.ac.il">bshaanan@bgu.ac.il</a>><br clear="none">>> Subject: Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18<br clear="none">>> Date: December 23, 2019 at 1:21:35 PM PST<br clear="none">>> To: "<a shape="rect" ymailto="mailto:chimera-users@cgl.ucsf.edu" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>" <<a shape="rect" ymailto="mailto:chimera-users@cgl.ucsf.edu" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br clear="none">>> <br clear="none">>> Hi,<br clear="none">>> <br clear="none">>> I ran into this Chimera/Delphi problem a few months ago (and discussed it with the Chimera/Delphi people). The latest Delphi version that I tried (8.4) produced a cube format file which formally can be read and contoured in the Chimera volume viewer. I hated the way the electrostatic surface produced that way looked and abandoned it. Delphi v. 6 which I have (and which I think Elaine used 3 years ago) produced the good old .phi which is file properly displayed in Chimera . I think one can still get hold of V.6 from the Delphi distribution site. <br clear="none">>> <br clear="none">>> To avoid this mess I used the APBS interface of Chimera which worked fine and produced a nice, familiar style, looking electrostatic surface (see for example Fig. S10 in the supplementary of doi: 10.1093/nar/gkz604).<br clear="none">>> <br clear="none">>> Regards,<br clear="none">>> Boaz<br clear="none">>> <br clear="none"><br clear="none"><br clear="none"><br clear="none"><br clear="none"></div></div></div>
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