[phenixbb] real_space_refine questions

Daniel Larsson daniel.larsson at icm.uu.se
Mon Jun 12 01:49:10 PDT 2017

I'm have some questions about doing real space refinements using phenix.real_space_refine. I am refining a model for an intermediate-resolution (3.79 Å) cryo-EM map. As the starting point I use a model from a higher-resolution map (3.25 Å) of the same system in another conformation. My idea is to first do rigid body fitting of domains and then gradually relax constrains and restraints.

- Is it possible to restrain the position of certain parts of the model (i.e. "freeze" them so that they move at all) to do focused refinement of subdomains or loops?

- In the instructions it says that you can do both NCS constraints and restraints. How you do the latter? I can only do the former by default or by defining ncs_constraints=True and give a NCS definition file.

- When I do a run with run=rigid_body, some rigid body groups move in to each other and overlap. Is there no collision detection using this algorithm? If I do a run=minimization_global, things work a bit better in this regard, but is not really what I want (at this stage). Am I doing something wrong? Here is the run command and the rigid body definition file:

phenix.real_space_refine \
    model.pdb \
    map.ccp4 \
    rigid.eff \
    resolution=8.0 \
    ncs_constraints=False \
    rotamer_restraints=True \
    ramachandran_restraints=True \
    c_beta_restraints=True \
    run=rigid_body \

# rigid.eff:
refinement {
    rigid_body {
    group = chain A and resseq 101:266
    group = chain A and resseq 273:388
    group = chain B and resseq 101:266
    group = chain B and resseq 273:388
    group = chain C and resseq 104:266
    group = chain C and resseq 273:388

Daniel Larsson

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