[Chimera-users] [chimera-dev] Visualize 3D structure of Peptide

[Elaine Meng]

Dear Reza,
This is not really a Chimera question.  You would need to go to the Protein DataBank website and search there.  Their searching is powerful and has many options, which you can explore:
<https://www.rcsb.org/#Category-search>

Another way is to search for your protein of interest at UniProt, then see if there are PDB IDs given in the structures section for that protein.  UniProt:
<http://www.uniprot.org/>

If there isn’t a known structure in the Protein DataBank, other possibilities are to:

(A) look in databases of comparative models, e.g. ModBase, from which you can download a PDB file to open in Chimera
<https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi>

(B) build comparative model yourself if the structure of a similar protein/peptide is known
<https://en.wikipedia.org/wiki/Homology_modeling>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>

(C) if it’s a pretty small peptide, build from scratch, but still difficult to know if the conformation is realistic without more work (dynamics etc.).  For example, Chimera allows you to build peptides (Tools… Structure Editing,... Build Structure; the Start Structure section includes a “peptide” option).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>

Finally, the chimera-dev e-mail address is for programming questions.  If you have user questions, for future reference the better address is chimera-users at cgl.ucsf.edu (CC’d on this message).
Good luck,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 21, 2018, at 10:25 PM, Mohammadreza Behi <m.behi at sydney.edu.au> wrote:
> 
> Dear Sir/Madam,
> I am trying to visualize a peptide and a protein using Chimera, yet I am not sure if the peptides may have an ID to fetch the structure by ID.
> Even I could not find the ID for my protein.
> Can you please let me know how I may find the ID for these items? Or if there is not any ID how to visualize them for further studies?
> Kind regards,
> Reza\