[Chimera-users] conjugate moiety to protein PDB

Eric Pettersen pett at cgl.ucsf.edu
Thu Jan 30 13:49:39 PST 2020

For #1 you could write a script that opens a tosyl moiety, uses the “combine” command to put it into the same model as the protein, then uses the “bond”, “adjust angle”, “adjust length” and “rotation” commands to bond the moiety to the cysteine, and adjust the bond angle, length, and torsion angle respectively.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jan 30, 2020, at 11:17 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Scott,
> The “Join Models” section of Build Structure is what you would use to attach moieties without placing them manually beforehand. It has a peptide bond option and a more general option:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>
> However, even without the need for any manual positioning, it still wouldn't be that convenient for repetitive use, because you’d have to keep opening the part you want to attach over and over as a new model, since attaching it moves it into the other model.  However, there is no command equivalent to Join Models.  Any high-throughput use would require python scripting and somebody else would have to advise on that.
> For task 1 specifically, modification of amino acid side chains, sometimes one can use the SwissSideChain plugin to Chimera.  It includes several nonstandard residues that can be substituted in with the “swapnaa” command (after the plugin has been installed), but it may not be useful in your case, as I don’t see any tosylated cysteine in their list of choices.
> <https://swisssidechain.ch/visualization/chimera.php>
> <https://swisssidechain.ch/browse/family/table.php?family=all>
> For task 2 specifically, if the peptide is already built separately, you would need to use Join Models as mentioned above.  However, you can also build outwards from an existing chain residue by residue with the “addaa” command.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jan 29, 2020, at 9:15 PM, Michael Scott Bowers <scott.bowers at northwestern.edu> wrote:
>> Hi power users,
>> I have 2 tasks that I hope you can help with. Both of these require conjugation of a moiety to multiple places on a large, multi chain protein. Command line solutions are fine. 
>> Task 1. Conjugate some group like a tosyl to selected cystine residues. There could be about 200 residues needing conjugation across 4 chains of a protein PDB file.
>> Task 2. Conjugate a peptide chain to the N or C terminus of a multi chain protein PDB file.  
>> I am already familiar with build structure protein and smiles, but connecting models without severe steric hindrance is problematic. Also, given the number of needed conjugations, it would be great it I could do this via command line (or some other function that I am currently not aware of) so that the tosyl or peptide chains needing connecting do not have to be positioned prior to making the covalent bond.
>> Much thanks to everyone in advance.
>> Best, 
>> Scott
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