[Chimera-users] New residues for swap commands

[Elaine Meng]

Hi Rodrigo,
It may be difficult to add your own, since it could involve understanding the code and defining multiple rotamers (conformations) of each side chain.  The swap commands are especially useful because they help choose among the multiple rotamers.  However, here are some other suggestions:

(1) If you get the SwissSidechain plugin for Chimera,
<https://swisssidechain.ch/visualization/chimera.php>

... it will allow using a different command "swapnaa" (non-natural amino acids) to substitute any of >200 non-natural amino acids that are in the SwissSidechain database:
<https://www.swisssidechain.ch/>

Browse that database to see what it includes:
<https://swisssidechain.ch/browse.php>

I'm not aware of any similar capability for nucleotides, however.

(2) if the new residue is similar to a standard residue or one available in the database above (e.g. you just need to add a methyl group or other small substituent, or change the element of an atom), it would be simpler just to change that residue one atom at a time in Chimera with the Build Structure tool (in menu under Tools.. Structure Editing), the Modify Structure section:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#modify>

(3) yet another possibility is if you have a PDB file that contains the nonstandard residue, you could match its backbone onto the position that you want to modify in the original, then save that PDB file relative to the original model, then manually text-edit a copy of the original model PDB file to substitute in the coordinates of the nonstandard residue from the PDB file you just saved.  You might need to do some other things like edit residue number and chain.  This is not too bad if you are rather familiar with PDB format..
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coords>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 15, 2022, at 10:19 AM, Rodrigo Galindo-Murillo via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello!
> Is it possible to add new amino acids to the swapaa and new
> nucleotides for the swapna commands?
> 
> Thank you!
> Rodrigo.