[phenixbb] ligand at two-fold

[Patrick Loll]

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This would seem to imply that the custom_nonbonded_symmetry_exclusions command is obsolete, but it’s still found in the list of all available keywords (?).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

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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