Hello All, I am currently solving a structure at 2A resolution with phases obtained from molecular replacement. Using the MR solution, I began refinement with Refmac using NCS restraints. I am currently building the parts of the model that were left out of the MR search model, and have just about successfully completed all three NCS-related chains. Obviously I will continue to use the most complete model for refinement, and plan to release the NCS restraints over the parts of the molecule that don't quite seem to obey perfectly.
My question is, once I have connected density for all three chains will it still be worthwhile to perform density modification, such as solvent flipping/flattening or histogram matching (implemented through SOLOMON and/or DM) to improve phases? It seems that I have always been told that density modification is typically carried out at the beginning of refinement, prior to any model building, however my understanding of these types of density modification (particularly solvent flipping/flattening) leads me to believe that they would be most effective when more of the molecular envelope can be identified, such as during later stages of refinement. Also, I read something recently that lead me to believe that the solvent flattening procedure may be implicit in the implementation of NCS averaging in refinement software. I understand that the two processes are fundamentally different and independent of one another, but the information I recently read described something like the following (unless I misinterpreted). Because real space NCS averaging requires identification of the molecular envelope in the same fashion as solvent flattening, during NCS averaging the envelope is identified then the map is solvent-flattened and averaged using the NCS operator. I am unfamiliar with the inner-workings of most crystallographic software, so I was wondering if this is how NCS averaging is implemented in Refmac? I suppose another way to ask the question would be: If I have an NCS-averaged map from Refmac, is it already solvent-flattened? Any help would be much appreciated. I am still relatively new to the refinement process. Thanks, Mike Thompson -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles [email protected]
