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?
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... On Fri, May 19, 2017 at 12:33 AM, Pavel Afonine <pafon...@gmail.com> wrote: > Just use P1 and "ncs" constraints. What's the problem? Or just keep entire > map and have only symmetry independent copy to work with until finishes, > then make the whole molecule. For real-space refinement it's totally > irrelevant whether you have whole molecule or 1/Nth of it. So.. it isn't > clear what the problem is.. > Pavel > > On Thu, May 18, 2017 at 10:06 PM, Qingfeng Chen <che...@gmail.com> wrote: > >> Hi, >> >> I have an EM map of a tetrameric protein. It was painful to work with >> this map since it is in P1 spacegroup, although 4-fold symmetry was already >> applied during map reconstruction. >> >> I noticed that people used MAPMAN to transform spacegroup, however, it >> seems not working for me. The map remained in P1 spacegroup afterwards. >> >> I used mtz file converted from .mrc and the tetrameric protein model as >> input and choose "run fft to generate simple map". I also specified "output >> map in ccp4 format to cover all atoms in pdb". In "infrequently used >> options", I input P4 in "generate map in spacegroup". Everything else was >> left as default. >> >> Any suggestions will be appreciated. >> >> Thanks! >> > >
