[phenixbb] individual plus group adp's

Pavel Afonine pafonine at lbl.gov
Tue Feb 17 09:17:26 PST 2009

Hi Emmanuel,

why don't you just do combined TLS + individual ADP refinement, which is 
the best option in most of cases?

Anyway, here is the answer to your question. If you are running 
phenix.refine from the command line, the following command

phenix.refine model.pdb data.hkl params.txt

where the file "params.txt" contains these lines

refinement.refine {
    strategy = *individual_sites rigid_body *individual_adp *group_adp tls \
               *occupancies group_anomalous
    adp {
      individual {
        isotropic = chain A or chain B
      group_adp_refinement_mode = one_adp_group_per_residue \
      group = chain C

will refine:
- individual coordinates for all atoms;
- individual isotropic B-factors for all atoms in chain A and B;
- group B-factor for chain C (one B-factors per whole chain C);
- occupancies for all atoms in alternative conformations (if any present 
in your structure).

Also should be able to do this using phenix.refine GUI.

Please let me know if you have any questions!


On 2/17/2009 7:47 AM, Manolis Saridakis wrote:
> Dear Colleagues, 
> I have a question that I guess has a simple answer which however I haven't been able to 
> find in the manual. I am using phenix.refine version 1.4. 
> My model has 3 chains + solvent and I would like to refine individual adp's for 
> everything except one of the chains, for which I would like to keep a group adp 
> refinement option. 
> My attempts have failed so far: depending on what exactly I do (which I guess there is 
> no point detailing here), I am either refining my other chains as groups too (i.e. the 
> same number is added to all adp's of the chain) or nothing stays grouped. However, in 
> the manual it does say if I am not mistaken that one can do what I want (but there is 
> no example of that situation). 
> Many thanks for your help! 
> Best wishes, 
> Emmanuel Saridakis 

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