[chimerax-users] Replacing regular residues with unusual ones

[Tristan Croll]

For completeness, there is one further way you can do this (using ISOLDE). Currenly slightly hacky, but it should work:

- change the residue name: select at least one atom, then “setattr sel residues name 2MR”
- remove its hydrogens: press up once to select the whole residue, then “del sel&H”
- open ISOLDE’s unparameterised residues widget (on the validation tab)
- choose the 2MR
- in the second table you’ll find a list of matching templates by name or partial topology. Choose the by-name one, and click the button to fix it. This should add in all the missing atoms with PDB-correct names.

> On 10 Feb 2021, at 03:33, anaa2 <anaa2 at mrc-mbu.cam.ac.uk> wrote:
> 
> 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
> 
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