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How to specify a specific rotamer

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How to specify a specific rotamer

I want Rosetta to use only a specific rotamer of Histidine that I have in a pdb when designing. Is there any way to do this? I have tried using SampleRotamersFromPDB but I am unsure how to provide the pdb and I get the following error:

I include this in the command line: -packing::unboundrot his_rotamer.pdb

Error messages were:

From line 12:

Error: Element 'SampleRotamersFromPDB': This element is not expected.


 7:             <ScoreFunction name="score" weights="ref2015"/>

 8:     </SCOREFXNS>


10:             <ReadResfile name="rr" filename="resfile_0.txt"/>

11:             <InitializeFromCommandline name="ifcl" />

12:             <SampleRotamersFromPDB name="his_rotamer.pdb"/>




Post Situation: 
Wed, 2018-02-21 20:35

Unfortunately, the SampleRotamersFromPDB operation isn't yet in the released version of Rosetta -- it's currently in a development branch and should hopefully be incorporated into a weekly release at some point in the near future. (There were a few last minute issues with associated code which resulted in a delay.) The documentation has laready been updated in anticipation of the release, though. We appologize for the inconvenience.

If you're not interested in waiting until it's released (and I wouldn't blame you), if you provide a bit more information about your use case I could try to suggest an alternative.

What I will say is that Rosetta typically will not touch a particular rotamer unless you let it. So if your input PDB contains that particular residue,  you can make sure that you always have a PreventResiduesFromRepacking task operation on for that residue. That should keep Rosetta from changing it during packing.

It won't necessarily keep it from moving during minimization, though. (Or if you miss a packing operation.)  One way to "fix" that is to add constraints to the residue. If you have dihedral constraints applied to the two sidechain chis for the residue you can bias them heavily toward that particular rotamer. That should keep both packing and minimization from changing the rotamer significantly, assuming that you're packing/minimizing with a scorefunction which has the dihedral_constraint scoretern turned on.

Thu, 2018-02-22 09:29