[chimerax-users] Replacing regular residues with unusual ones

[Elaine Meng]

Hi Noor,
Sometimes you can do this in Chimera with the SwissSidechain plugin.  However,

(1) this plugin is not available for ChimeraX
(2) it does not include the specific unusual residue you are asking about, dimethylarginine 
(pdb 2MR <http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=2mr&operation=ccid>)

In case anybody else is interested, the plugin is described/available here:
<https://swisssidechain.ch/visualization/chimera.php>

...and you can browse the database of unusual amino acids, for example arginine derivatives
<https://swisssidechain.ch/browse/family/table.php?family=arginine>

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

> On Feb 9, 2021, at 5:52 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Hi Noor,
> 	No, swapaa cannot do that.  However, you could use the "Build Structure" tool (in the Structure Editing category) to modify a normal arginine into 2MR.  You would select the NH1 and change it to be trigonal with three bonds (which will add two hydrogens), then select a hydrogen and change it to be a tetrahedral carbon named CQ1 with 4 bonds (i.e. a methyl group).   Do a similar sequence with the NH2.  Before you make any changes, ensure that the "Residue Name" section of the tool is set to "Change modified residue's name to 2MR".
> 
> --Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
>> On Feb 9, 2021, at 5:29 PM, anaa2 <anaa2 at mrc-mbu.cam.ac.uk> wrote:
>> 
>> Hi,
>> In ChimeraX can a regular residue be replaced with an unusual one using the swapaa function(pdb code 2MR)?
>> Best wishes,
>> Noor