Hi Phil, the only way to do it phenix.refine is to assign different altlocs to overlapping atoms, say A to one domain and B to another one. Then they will not "see" each other via non-bonded interactions. Also, in this case phenix.refine will refine occupancies of these atoms (which you can turn off if you wish). I guess by default it will group occupancies such that A+B=1 per residue frame (may be not, I forgot how I implemented it). That is for instance adjacent residues within A conformer may have different occupancies; same for B. Perhaps in your case you don't want this: having all occupancies to be equal within each conformer would make more sense. You can do it by using this syntax: refinement.refine { occupancies { constrained_group { selection = chain A and resseq 1:100 and altloc A selection = chain B and resseq 1:100 and altloc B } } } In this case all atoms in (chain A and resseq 1:100 and altloc A) will have the same occupancy between 0 and 1, and same for (chain B and resseq 1:100 and altloc B); and constraint occupacy_of(A) + occupancy_of(B)=1 will be used. Let me know if you need any help with this. Pavel On 2/1/13 12:58 PM, Phil Jeffrey wrote:
Hi,
I've got a pernicious problem where the electron density for one domain appears to extensively interpenetrate another similar domain. I'm in the process of trying to work out things like: MR solution in the wrong space group courtesy of pseudo-centering. In the meanwhile I want to model it as interpenetrating domains, and need to turn off VdeW bumps at the domain (chain) level of structure. I can't just model it as a infinite list of alternate locations.
I (think) I remember how to do this in CNS (constraints interaction), but is there a way to do this in phenix ? I could not track down a particularly promising section of either the manual or the .def/eff file(s).
Thanks Phil Jeffrey Princeton _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb