[phenixbb] ligand at two-fold

[Pavel Afonine]

Hi Pat,

your are on the right track handling this issue with a nuance that 
causes the failure.. If you specify the parameter file, then unlike 
command line, it has to specify the compete parameter name (include 
parent scopes of the parameter in question), in your case

refinement.pdb_interpretation.custom_nonbonded_symmetry_exclusions="chain X"

Let me know if that doesn't do it and I will have another look!

Pavel

On 4/14/22 12:59, Patrick Loll wrote:
> Hello all,
>
> I have a dimer in which the two protomers are related by a crystallographic 2-fold. There is a peptide ligand that sits in the interface between the two protomers. This means that the ligand will be present in two orientations, and I’ve set the occupancies to 0.5. However, the ligand is pushed out of density during refinement, presumably because orientation #1 is repelling orientation #2 (to be clear, orientations #1 and #2 are symmetry mates).
>
> To deal with this, I include a parameter file in the GUI that contains the following instruction:
>
> custom_nonbonded_symmetry_exclusions = "chain X”       [where chain X is the peptide ligand]
>
> However, the refinement fails, with the following error message:
>
> "Unused parameter definitions: Please check the input file(s) for spelling errors and obsolete parameter definitions."
>
> This would seem to imply that the custom_nonbonded_symmetry_exclusions command is obsolete, but it’s still found in the list of all available keywords (?).
>
> Any help would be welcome.
>
> Thanks,
>
> Pat
>
> ---------------------------------------------------------------------------------------
> Patrick J. Loll, Ph. D.  (he, him, his)
> Professor of Biochemistry & Molecular Biology
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St., Mailstop 497
> Philadelphia, PA  19102  USA
>
> pjl28 at drexel.edu
> pjloll at gmail.com
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