[chimerax-users] Replacing regular residues with unusual ones

[anaa2]

Hi,

Just to update everyone. Tristan's suggestion below worked. Thank 
goodness for ISOLDE and ChimeraX. Thank you, everyone.

Best wishes,
Noor

On 10.02.2021 07:49, Tristan Croll wrote:
> 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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