<html><head></head><body><div class="ydp87d8434byahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;"><div><div dir="ltr" data-setdir="false">OK,</div><div dir="ltr" data-setdir="false">I tried all the three academic versions of DelPhi for windows; and none is working for me. I contacted the DelPhi supporters and SUGGESTED to use CUBE output format which isn't possible in Chimera. In the mean time, the two Chimera versions I installed read 3eeb.phi file from the tutorial. </div><div dir="ltr" data-setdir="false">I will report the problem.</div><div dir="ltr" data-setdir="false">regards,</div><div><br></div><div class="ydp87d8434bsignature"><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 Monday, December 23, 2019, 08:30:26 PM GMT+3, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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<div><div dir="ltr">It should be any DelPhi version that you get from the academic website, which was a link in this page I sent earlier:<br clear="none"><br clear="none">> The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here:<br clear="none">> <<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp</a>><br clear="none"><br clear="none">…specifically this is their academic website <<a shape="rect" href="http://compbio.clemson.edu/delphi" target="_blank">http://compbio.clemson.edu/delphi</a>><br clear="none"><br clear="none">I don’t remember what version I used several years ago to make 3eebB.phi, but as far as I know the format didn’t change. It is possible it changed and we didn’t know about it, but we would need example(s) of the files.<br clear="none"><br clear="none">If you believe you used the academic version of DelPhi but you get the error opening the phi file, you could try using Chimera menu Help… Report a Bug and attach your phi file so we could take a look at it. However, that does not guarantee it will be possible to fix.<br clear="none"><br clear="none">I hope this helps,<br clear="none">Elaine<br clear="none"><div class="yqt4279176222" id="yqtfd95701"><br clear="none">> On Dec 22, 2019, at 4:23 AM, labe boye <<a shape="rect" ymailto="mailto:sintaspirulina@gmail.com" href="mailto:sintaspirulina@gmail.com">sintaspirulina@gmail.com</a>> wrote:<br clear="none">> <br clear="none">> Hi<br clear="none">> Thank you for your reply.<br clear="none">> Could you please let me know which version of DelPhi academic version is compatible with Chimera? Which DelPhi version was used to generate the 3eeb.phi file in the tutorial?<br clear="none">> kindest regards,<br clear="none">> <br clear="none">> On Fri, Dec 20, 2019 at 11:16 PM 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">> Hi,<br clear="none">> Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry. <br clear="none">> <br clear="none">> The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here:<br clear="none">> <<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp</a>><br clear="none">> <br clear="none">> If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it.<br clear="none">> <br clear="none">> Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read:<br clear="none">> <<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html</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">> <br clear="none">> > On Dec 20, 2019, at 10:33 AM, labe boye <<a shape="rect" ymailto="mailto:sintaspirulina@gmail.com" href="mailto:sintaspirulina@gmail.com">sintaspirulina@gmail.com</a>> wrote:<br clear="none">> > <br clear="none">> > Hi,<br clear="none">> > I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error<br clear="none">> > Error reading file default.phi, format delphi<br clear="none">> > Record size > file size <br clear="none">> > What is the solution?<br clear="none">> > regards,<br clear="none">> > <br clear="none">> <br clear="none">> <br clear="none">> <br clear="none">> -- <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">> The bamboo that bends is stronger than the oak that resists </div><br clear="none">> _______________________________________________<br clear="none">> Chimera-users mailing list: <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">> Manage subscription: <a shape="rect" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><div class="yqt4279176222" id="yqtfd09640"><br clear="none"></div></div></div>
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