Hi Colin, just to add to Ralf's reply... If you need an example, here is file containing atoms in alternative conformations that will be automatically recognized by phenix.refine: http://www.rcsb.org/pdb/files/1a6m.pdb Currently phenix.refine can do the following types of occupancy refinement: 1) Individual (just refine occupancies of atoms without any restrictions); 2) Group (refine one occupancy per selected group of atoms). Example: ATOM 6 S SO4 1 1.302 1.419 1.560 0.70 10.00 S ATOM 7 O1 SO4 1 1.497 1.295 0.118 0.70 10.00 O ATOM 8 O2 SO4 1 1.098 0.095 2.140 0.70 10.00 O ATOM 9 O3 SO4 1 2.481 2.037 2.159 0.70 10.00 O ATOM 10 O4 SO4 1 0.131 2.251 1.823 0.70 10.00 O 3) Constrained individual: refine occupancies of n atoms making sure that the sum of occupancies over all n atoms is equal to 1.0. What is not yet available (although almost done) is constrained group occupancy refinement; this is similar to "3)": refine one occupancy per group of atoms making sure that the occupancies are equal to each other within the group and the sum of the occupancies for an atom is 1.0. Example: ATOM 6 S ASO4 1 1.302 1.419 1.560 0.70 10.00 S ATOM 7 O1 ASO4 1 1.497 1.295 0.118 0.70 10.00 O ATOM 8 O2 ASO4 1 1.098 0.095 2.140 0.70 10.00 O ATOM 9 O3 ASO4 1 2.481 2.037 2.159 0.70 10.00 O ATOM 10 O4 ASO4 1 0.131 2.251 1.823 0.70 10.00 O ATOM 11 S BSO4 1 3.302 3.419 3.560 0.30 10.00 S ATOM 12 O1 BSO4 1 3.497 3.295 2.118 0.30 10.00 O ATOM 13 O2 BSO4 1 3.098 2.095 4.140 0.30 10.00 O ATOM 14 O3 BSO4 1 4.481 4.037 4.159 0.30 10.00 O ATOM 15 O4 BSO4 1 2.131 4.251 3.823 0.30 10.00 O I'm working on this right now and hopefully it will be available soon. Pavel. Dr. Colin W. Levy wrote:

Hi,

What is the correct procedure in phenix for dealing with alternative conformations of side chains?

Thanks

Colin _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb