Hi, explore and use more tools in phenix.refine that are not used by default, such as: - automated water picking and refinement (ordered_solvent=true); - TLS; - fix_rotamers; - if you get the latest development version then it will use the advanced real-space refinement (lockit) running by default as part of refinement run; - iterate this with manual building/rebuilding, ... etc. Pavel. On 12/7/10 6:10 AM, intekhab alam wrote:
Hi I am trying to solve the structure of RNA polymerase in complex with its protein primer. The size of protein primer is 70 amino acids which i complexed with the polymerase and collected a data of the complex crysta at 2.3A. The space group is C2 and after Molecular replacemnet with full length polymerase in auto MR i got 3 subunits in ASU. The parameters of MR solution RFZ=71.5 TFZ=41.2 PAK=0 LLG=8812 suggests that the solution is correct. I used autobuild for model building which gave me the model of the polymerase as well as some extra density that i am considering as the other protein. After several round of refinemnt i have R and R free of 27and 32 respectively. My queries: 1. I want to know ,how can i improve my R as well as R free. 2. How can i model other protein as the density is weak and not complete, how can i improve the map of the other protein so that i can b ebale to trace the c-alpha backbone, i was able to model only 10 amino acids so far.