[Chimera-users] Visualizing gaussian output files in UCSF chimera

[Anthony James Schaefer]

Prathvi,

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.

You can also try to use the ChimAARON plugin for Chimera (https://github.com/QChASM/SEQCROW/tree/Chimera). 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.

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.

Best,

Tony
________________________________
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Tuesday, January 18, 2022 7:59 PM
To: Prathvi Singh <prathvi at iitk.ac.in>
Cc: chimera-users at cgl.ucsf.edu List <chimera-users at cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer at uga.edu>
Subject: Re: [Chimera-users] Visualizing gaussian output files in UCSF chimera

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi Prathvi,
Just FYI, if you use our ChimeraX program and install the SEQCROW<https://cxtoolshed.rbvi.ucsf.edu/apps/seqcrow> plugin from the ChimeraX Toolshed<https://cxtoolshed.rbvi.ucsf.edu/>, then ChimeraX will be able to open/display Gaussian .log files.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

On Jan 18, 2022, at 9:34 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>> wrote:

Hi Prathvi,
Sorry no, Chimera does not read Gaussian log files.  Here's the page listing the formats Chimera knows:

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>

For Gaussian, I only see "Gaussian formatted checkpoint" (.fchk) and "Gaussian cube grid" (.cube, .cub).

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 18, 2022, at 4:47 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>> wrote:

Hello again Elaine,

I have one more question. Is there a way to open & visualize a gaussian output file (it has extension of .log) in UCSF chimera?

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?

Thanks again & always

--
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016


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