[phenixbb] fixing atoms during refinement

[Pavel Afonine]

Hi,

thank you for your question.

Fixing atomic parameters in refinement (xyz, ADP, occupancies, rigid body parameters, etc.) is a new feature that was added a few days ago. 

The official latest PHENIX release does not have this feature yet;  however if you get the latest CCI APPS (subset of PHENIX, containing HySS, phenix.refine, eLBOW, Xtriage, ...; look "Quick Facts" for more info) you can use the "latest & greatest" features.

Please  go to http://www.phenix-online.org/download/cci_apps  and get the latest CCI APPS. For more information, you can check out the updated "Documentation" and "Quick Facts" (right next to phenix.refine link).

Fixing atomic parameters in refinement (in a few words; this will be added to the Manual shortly):
With the latest version of CCI APPS it is possible to refine any part of a model parameters in any combination as:
- individual sites;
- individual ADP (iso-, aniso-, both or mix);
- individual occupancies;
- rigid body;
- TLS;
- group isotropic ADP;

Also it can be combined with water picking and simulated annealing. For example, this powerful sequence can be done in one refinement run (and in right order):
“rigid body + SA + group B + individual B and TLS + individual XYZ + water picking”.

Now, for a practical example, If you look at the parameters (type phenix.refine --show-defaults=all), among others you will find these lines:

....
refinement.refine {
  strategy = *individual_sites rigid_body *individual_adp group_adp tls \
             individual_occupancies group_occupancies none
  sites {
    individual = None
    rigid_body = None
  }
  adp {
    individual {
      isotropic = None
      anisotropic = None
      force_all_to_be_refined_isotropically = True
    }
    group = None
    one_adp_group_per_residue = True
    tls = None
  }
  occupancies {
    individual = None
    group = None
  }
}
...

Here is the example that I think will give you an idea how this works:
if your molecule has three chains: A, B and chain C, then the following command:

phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp+tls sites.rigid_body="chain A" sites.individual="chain B" adp.tls="chain A" adp.tls="chain C"

will do the following:
   - refine chain A as a rigid body;
   - refine individual isotropic B-factors for the whole molecule;
   - refine individual coordinates for chain B;
   - refine TLS parameters for chain A and chain C.

Now to add automatic water picking, just add ordered_solvent=true line to the command above:

phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp+tls sites.rigid_body="chain A" sites.individual="chain B" adp.tls="chain A" adp.tls="chain C" ordered_solvent=True

Please check out the Documentation for more refineemnt strategies and selection examples.

Ok, I hope this is enough to get started. 
Please don't hesitate to ask more questions or report any bug or if whatever I tried to explaine is not clear. 

Thanks again for your question,
Pavel.