[Chimera-users] displaying backbone atoms of peptide

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 12 11:33:24 PDT 2016


Hi Jesse,
Well, you’d have to work out what structure you want in terms of the chemistry.  Then you could do some combination of changing atom types and building outwards gradually with the Modify Structure section of Build Structure, and opening “pieces” as separate models (for example, opening the fullerene structure separately) and then joining them together with the Join Models section of Build Structure. These tools take some practice getting used to, you would probably need to play around with them for a while.  At least there is full documentation:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>

Not sure where you could get the fullerene 3D coordinates, if you don’t already have them.  I saw there were fullerenes in PubChem, but when I tried pubchem fetch in Chimera, their 3D structures (at least the ones I tried) were not available using that method.  Then I found this database with downloadable structures in “xyz” format but it was not the “xyz” format Chimera expected and could not be opened in Chimera:
<http://www.nanotube.msu.edu/fullerene/fullerene-isomers.html>

If you’re OK doing a little text-editing, you can fix this problem by simply removing the extra 4 columns of numbers at the ends of the atom lines in the xyz file from that database, and then open the xyz file in Chimera.

Otherwise, you could use format-converting site to convert from xyz to pdb, and then open the resulting pdb in Chimera.  
<http://nl.webqc.org/molecularformatsconverter.php>

… still somewhat laborious in that you have to paste in the contents of the xyz file (downloaded from that database, name ends in .xyz) and then copy and paste the output in a text-editor to create the pdb file (plain text file, name ends in .pdb), but not too bad if you’re only going to do it once or a few times.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 12, 2016, at 9:18 AM, Jaynes, Jesse <jjaynes at mytu.tuskegee.edu> wrote:

> Hi Elaine:
> Thank you so much!  You have been extremely helpful.
> 
> I also was wondering how I might attach a fullerene with a peptide?  I was going to do it through a sulfhydryl and an amino on the fullerene.  Any ideas about how to do that?  Thank you, Jesse
> 




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