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Prathvi,</div>
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SEQCROW does not parse residue information from Gaussian output files, so it might not be what you want. I believe parsing residue data is in the works, but I don't have an estimate for when it will be in SEQCROW.
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You can also try to use the ChimAARON plugin for Chimera (<a href="https://github.com/QChASM/SEQCROW/tree/Chimera" id="LPNoLPOWALinkPreview">https://github.com/QChASM/SEQCROW/tree/Chimera</a>). ChimAARON is a precursor of SEQCROW. I'm not developing it anymore,
and it also doesn't parse residue data. In ChimAARON, Gaussian output files should be specified as an "AaronTools coordinate" file. The ChimAARON installation process is a bit more perilous than SEQCROW's, but there's a guide about 2/3 of the way down that
page. <br>
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In the version of AGUI I have access to, I can save a PDB file with the residue data. I think GaussView and AGUI are basically the same, but perhaps they differ in what file types they can save.
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Best,</div>
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Tony<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, January 18, 2022 7:59 PM<br>
<b>To:</b> Prathvi Singh <prathvi@iitk.ac.in><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu><br>
<b>Subject:</b> Re: [Chimera-users] Visualizing gaussian output files in UCSF chimera</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space"><font color="BA0C2F">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]</font><br>
<br>
<div>Hi Prathvi,
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Just FYI, if you use our ChimeraX program and install the <a href="https://cxtoolshed.rbvi.ucsf.edu/apps/seqcrow" class="">SEQCROW</a> plugin from the <a href="https://cxtoolshed.rbvi.ucsf.edu/" class="">ChimeraX
Toolshed</a>, then ChimeraX will be able to open/display Gaussian .log files.</div>
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<div class="">
<div class="">--Eric</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jan 18, 2022, at 9:34 AM, Elaine Meng via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
<div class="">
<div class="">Hi Prathvi,<br class="">
Sorry no, Chimera does not read Gaussian log files. Here's the page listing the formats Chimera knows:<br class="">
<br class="">
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html</a>><br class="">
<br class="">
For Gaussian, I only see "Gaussian formatted checkpoint" (.fchk) and "Gaussian cube grid" (.cube, .cub).<br class="">
<br class="">
Best,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D. <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
<blockquote type="cite" class="">On Jan 18, 2022, at 4:47 AM, Prathvi Singh via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:<br class="">
<br class="">
Hello again Elaine,<br class="">
<br class="">
I have one more question. Is there a way to open & visualize a gaussian output file (it has extension of .log) in UCSF chimera?<br class="">
<br class="">
I found that if you convert the .log file to .mol file using gaussian's software GAUSSVIEW, you can visualize the .mol file in chimera. However, the identity of the residues is lost; all the residues are shown as UNK. Is there a better way to do this?<br class="">
<br class="">
Thanks again & always<br class="">
<br class="">
-- <br class="">
Prathvi Singh,<br class="">
Research Fellow,<br class="">
Department of Biological Sciences & Bioengineering,<br class="">
Indian Institute of Technology, Kanpur-208016<br class="">
</blockquote>
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