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@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&targe...>) 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@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@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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