Hi, I'm working on the refinement of a protein mutated with an unnatural amino acid that is present as two rotamers. Whenever I do refinements, one of the rotamers moves away from the electron density map. I therefore would like to fix the coordinates for this amino acid only while continuing the refinement of the rest of the protein. Is there a way in Phenix to do this? Any advice is welcome. Best regards, Anna-Carin
Hi Anna-Carin,
According to documentation (
https://www.phenix-online.org/documentation/reference/refinement.html#refine...
):
Refinement with minimization (selected part of model):
% phenix.refine data.hkl model.pdb strategy=individual_sites \
sites.individual="chain A"
This will refine the coordinates of atoms in chain A only.
In your case selection would look more like sites.individual='not (chain A
and resid 123)' given you want to exclude residue with number 123 in chain
A.
In GUI (latest version), go to "Refinement settings" tab, button "Select
Atoms", "Refinement Strategy" tab and put the selection there.
Hope this helps,
Best regards,
Oleg Sobolev.
On Thu, Oct 27, 2016 at 8:52 AM, ancacarl
Hi,
I'm working on the refinement of a protein mutated with an unnatural amino acid that is present as two rotamers. Whenever I do refinements, one of the rotamers moves away from the electron density map. I therefore would like to
fix the coordinates for this amino acid only while continuing the refinement of the rest of the protein. Is there a way in Phenix to do this? Any advice is welcome.
Best regards,
Anna-Carin
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
I think it would be better to understand why phenix.refine is pushing one conformer out of density while leaving the other in. There is likely some problem with the ideal geometry definition or with your description of the alternative conformations. Forcing phenix.refine to accept your model, as is, prevents it from properly optimizing the side chain. Dale Tronrud On 10/27/2016 8:52 AM, ancacarl wrote:
Hi,
I'm working on the refinement of a protein mutated with an unnatural amino acid that is present as two rotamers. Whenever I do refinements, one of the rotamers moves away from the electron density map. I therefore would like to
fix the coordinates for this amino acid only while continuing the refinement of the rest of the protein. Is there a way in Phenix to do this? Any advice is welcome.
Best regards,
Anna-Carin
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
I agree, while technically it is possible to stop selected atoms from moving during refinement, it is much better to find out why refinement wants to move them (in a wrong place, as you seem to believe). If you send me model (before and after refinement) and data files, and tell what residue you are looking at, then I might be able to tell what's going on.. Pavel On 10/27/16 21:19, Dale Tronrud wrote:
I think it would be better to understand why phenix.refine is pushing one conformer out of density while leaving the other in. There is likely some problem with the ideal geometry definition or with your description of the alternative conformations. Forcing phenix.refine to accept your model, as is, prevents it from properly optimizing the side chain.
Dale Tronrud
On 10/27/2016 8:52 AM, ancacarl wrote:
Hi,
I'm working on the refinement of a protein mutated with an unnatural amino acid that is present as two rotamers. Whenever I do refinements, one of the rotamers moves away from the electron density map. I therefore would like to
fix the coordinates for this amino acid only while continuing the refinement of the rest of the protein. Is there a way in Phenix to do this? Any advice is welcome.
Best regards,
Anna-Carin
participants (4)
-
ancacarl -
Dale Tronrud -
Oleg Sobolev -
Pavel Afonine