[chimerax-users] Replacing regular residues with unusual ones

[anaa2]

Hi everyone,

Thank you. I tried the plugin, Elain. It didn't have 2MR in there. So I 
did as Eric suggested and it works. I will try the SEQCROW plugin that 
Tony developed later on. Many thanks, everyone for all your help.

Best wishes,
Noor

On 10.02.2021 02:35, Elaine Meng wrote:
> 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