Yes, that is what I have been doing. Build one subunit and assemble into > tetramer before realspace refinement (with "ncs" constraints). I used > tetramer for refinement because I want the distances between the inter > subunits interaction partners to be considered. The problem is, whenever I > want to make some manual adjustments of the model afterwards, I have to > break it into monomer and repeat the whole process again. I assume if the > map is in P4 spacegroup, I only need to modify one subunit of this protein > and changes will be automatically applied to the other subunits. Am I > right? >
So you have 4 copies and NCS group consisting of one master (or reference) copy and three related by NCS symmetry. Then you make changes in master copy and when you run refinement with NCS constraints the changes will be propagated onto the related copies by applying NCS constraints. This is how this works in phenix.real_space_refine. So no need to make identical changes in all 4 copies or go to P4. > Another question is, when I tried to refine my model using phenix > realspace refinement (energy minimization and adp), the statistics > generally become better (map CC, rotamer outlier etc), however, the > ramachandron statistics become worse, with increase number of outliers > (from below 1% to around 5%) and allowed (from several percent to 10-20%). > Do you know what could be the cause? I know I am asking the right person... > This is not expected (about worsening Ramachandran plot outliers). I'm sure we can solve this problem if you send me model and map files (and resolution) off list (if files too large to send by email please use Dropbox or similar file sharing tools). Pavel
