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

[Prathvi Singh]

Cool, thanks!

On Wed, Jan 19, 2022 at 7:47 AM Anthony James Schaefer <
tony.schaefer at uga.edu> wrote:

> 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> 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> 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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>

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