[Chimera-users] Ribbon Structures From Gaussian Output

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 30 16:00:59 PDT 2011

Hi Michael,
Chimera can read molecular structures from Gaussian "formatted checkpoint" files, but as you surmised, that would not give the standard peptide atom and residue names used for ribbon generation.  The whole structure would be placed in a single residue named UNK rather separated into its constituent amino acid residues for easy selection and command-line specification.

For all of that in Chimera, you would like to reformat the coordinate information from Gaussian into PDB format and change atom and residue names to the standard PDB amino acid atom and residue names.  I don't know if a program to do all of that exists... it would have to recognize the peptide substructures.   Maybe Babel could do it.  You could try asking on these forums (fora?):

Computational Chemistry List (ccl.net)
PDB Discussion Forum (pdb-l at rcsb.org)

Or, maybe Gaussian has some other output options besides formatted checkpoint that would get you closer to where you need to be.

Certainly you could read a Gaussian formatted checkpoint into Chimera and then write the structure out as PDB.  That would create correct PDB format in terms of the column placement and such, but you would still need to edit the atom names, residue names, and residue numbers to make it like a standard "peptide" PDB file.  Not too bad to do it by hand if you have only a few small structures, but it would become tedious for more or larger.

The PDB website has the definitive description of PDB format, but the Chimera documentation includes a summary "intro to PDB format":

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 30, 2011, at 2:49 PM, Michael Lodewyk wrote:

> Hello,
> I'm interested in using Chimera to visualize oligopeptide structures computed with Gaussian09 as ribbon structures... that is I'd like to be able to render an alpha helix backbone as a ribbon and then select specific residues/ligands to be rendered as tube or ball & stick models.  While I can save or convert the Gaussian output file to a variety of formats, they do not inherently contain the information necessary for such a rendering of the structure, as one would find in a true .pdb file.
> So my question is... Is Chimera the correct place to start for creating such representations?  If so, can you please point me to any documentation that would assist me in doing so?
> Thank you,
> Dr. Michael Lodewyk
> Tantillo Group, UC Davis

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