Visualizing gaussian output files in UCSF chimera
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
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@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
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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@cgl.ucsf.edu> Sent: Tuesday, January 18, 2022 7:59 PM To: Prathvi Singh <prathvi@iitk.ac.in> Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@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@cgl.ucsf.edu<mailto:chimera-users@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@cgl.ucsf.edu<mailto:chimera-users@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Cool, thanks! On Wed, Jan 19, 2022 at 7:47 AM Anthony James Schaefer < tony.schaefer@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@cgl.ucsf.edu> *Sent:* Tuesday, January 18, 2022 7:59 PM *To:* Prathvi Singh <prathvi@iitk.ac.in> *Cc:* chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
participants (4)
-
Anthony James Schaefer -
Elaine Meng -
Eric Pettersen -
Prathvi Singh