Dear all, in my electron density I can see negative difference density (fo-fc) for the carboxyl groups of some aspartates or glutamates. Assuming that this is a result of partial decarboxylation due to radiation damage, I wanted to refine the occupancies of these carboxyl groups. To this end, I set the occupancy of these atoms to 0.99 in Coot so that they would be picked up by occupancy refinement in phenix.refine (using version 1.4-3). Phenix however just put the value back to one. It looks like the occupancy refinement in phenix is meant for alternative conformations where the sum of the occupancies of the different conformations is 1. How can I make phenix refine partially decarboxylated acidic side chains? It does not seem appropriate to me to make alternative conformations, one with and one without the carboxyl group. That would look funny at my resolution (2.7 Angstrom) and might not fix the problem. Any hints are appreciated. Thank you, Nicole ---- Nicole Bischoff, M. Sc. PhD student in the Gruetter lab Department of Biochemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland +41 44 635 5556 [email protected]
Hi Nicole,
To this end, I set the occupancy of these atoms to 0.99 in Coot so that they would be picked up by occupancy refinement in phenix.refine (using version 1.4-3). Phenix however just put the value back to one. It looks like the occupancy refinement in phenix is meant for alternative conformations where the sum of the occupancies of the different conformations is 1.
No, phenix.refine can do individual, group, group constrained occupancy refinement. If it put the value back to 1, then this means that this is what it wants to refine to. By the way, setting it to .99 is one way of prompting phenix.refine to refine it. The other way is just give it a selection of atoms for which you want to refine occupancies, for example: phenix.refine model.pdb data.mtz refine.occupancies.individual="chain X and resseq 123 and name OXT" Since occupancies and B-factors are correlated, you can try to re-set b-factors to some average value, and try again. Also, you may try different staring value, say 0.5, and not .99. Pavel.
Hi I'm running Phenix Version: 1.4 Release tag: 3 doing a refinement with experimental phase restraints (HL coefficients) Are the experimental phases now included in the map coefficients? If so, with what weight? Are there parameters affecting this? I'm asking because there is one region of the map where the experimental phased density is significantly different from the model (perhaps from non-isomorphism of the major derivative), and in the map from phenix.refine the electron density follows the model, whereas in refmac, which does generate phase-combined map coefficients, the map density follows the experimental phases. (probably I shouldn't be using this non-isomorphous derivative in the refinement, but that's a different question) Phil
Hi Phil,
Are the experimental phases now included in the map coefficients?
Yes, this map is computed by default if input data file contains HL coefficients. The map coefficients file contains both, regular maps (2FOFCWT_no_fill and FOFCWT_no_fill) and the maps computed using modified set of Fobs (missing Fobs are substituted with <Fobs>; 2FOFCWT and FOFCWT). If HL are present then all these maps are phase-combined.
If so, with what weight?
What you mean by weight?
Are there parameters affecting this?
No. Pavel.
participants (3)
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Nicole Bischoff -
Pavel Afonine -
Phil Evans