Replacing regular residues with unusual ones
Hi,
In ChimeraX can a regular residue be replaced with an unusual one using the swapaa function(pdb code 2MR)?
Best wishes, Noor
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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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
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@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
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&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@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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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&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@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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Noor,
My SEQCROW plugin can technically do this, but Eric and Elaine's methods are probably easier for this type of thing.
You have to add the 2MR side chain to the substituent library:
1. Tools -> AaronTools -> Add to Personal Library 2. select side chain of a 2MR residue 3. give it a name, ignore conformer stuff (it's only used by another program) 4. click 'add current selection to library'
Before you do this, you might also need to set a directory for SEQCROW to store substituents. This is called 'Personal AaronTools library folder' in the 'SEQCROW' section of ChimeraX's settings. Then, chain a residue into 2MR with SEQCROW's change substituent tool:
1. Tools -> Structure Editing -> Change Substituents 2. select beta carbon on the residue 3. if you're worried about steric clashing, check 'relax substituent' 4. enter a new residue name 5. click 'substitute current selection'
The atoms will have the wrong names. I've been playing around with making SEQCROW aware of proximity names, so it'll automatically use CB, CG, CD, etc. If you want to try that, you can get SEQCROW from the dev branch on GitHub: https://github.com/QChASM/SEQCROW/tree/dev
If you scroll down on that page, there's instructions on how to install it. Note that this version only works with recent daily builds of ChimeraX. You'll also have to check 'use distance labels' on the change substituents tool.
Best,
Tony
________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of anaa2 anaa2@mrc-mbu.cam.ac.uk Sent: Tuesday, February 9, 2021 8:29 PM To: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Replacing regular residues with unusual ones
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Hi,
In ChimeraX can a regular residue be replaced with an unusual one using the swapaa function(pdb code 2MR)?
Best wishes, Noor _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (5)
-
anaa2 -
Anthony James Schaefer -
Elaine Meng -
Eric Pettersen -
Tristan Croll