[phenixbb] group_adp default ? and other phenix questions?

[Pavel Afonine]

Hi,

> Hi I quite new to the phenix environemnt and just ran a phenix 
> refinement with the following command line
>
> *_phenix.refine  myfile.mtz  mymodel.pdb simulated_annealing=true 
> model.ncs refinement.main.ncs=true --overwrite 
> refinement.ncs.excessive_distance_limit=None  >phenix_06_18_2008_2.log _*
>
> The model.ncs file is structured as follows
>
> refinement.ncs.restraint_group {
>   reference = chain A
>   selection = chain B
>   selection = chain C
>   selection = chain D
>       }

this looks good.

> My data is good to 3.3 A ( membrane protein)  and thus far I have been 
> refining with refmac5. After the phenix run indicated above,  I had a 
> dramatic reduction in r/rfree  ( post refmac 33/36 AND post phenix 
> 28/31). This is despite relatively small changes to my model by the 
> simulated annealing refinement.

This sounds great!

> 1) At my resolution I guess I should at best be refining only one 
> B-factor / ADP per residue is this the default behavior with the 
> command line above

No. By default, phenix.refine does individual ADP and coordinates 
refinement. The R/Rfree ~ 28/31 does not indicate an overfitting so you 
are most likely ok refining individual ADP. Of course it costs nothing 
to try to refine group ADP with one B per residue and the compare the 
results. At 3.3A it is not given that you must refine group B, refining 
individual B may be good too (as it looks like in your case).

BTW, I would also include refinement of TLS parameters which is good at 
this resolution.

> 2) I have seen the emails about syntax for forcing group-B refinement 
> at this location 
> <http://www.phenix-online.org/pipermail/phenixbb/2007-March/000161.html> 
> and this one 
> <http://www.phenix-online.org/download/documentation/cci_apps/structure_refinement.html> 
> .
> Basically they use strategy=group_adp . I am imagining this calculates 
> one ADP per residue or per defined group.  In my case if I force the 
> behavior with the syntax , how is group ADP for NCS-mates handled?

NCS restraints are not applied to B-factors if you refine them as 
"group_adp".

> 3) On a general note , when I say phenix.refine --show-defaults , the 
> section on strategy has a long list, what do the asterisks (*) in the 
> syntax mean .Does that mean those are the defaults .

"*" means selected. For example, by default you see:

strategy = *individual_sites rigid_body *individual_adp group_adp tls \
               *occupancies group_anomalous

which means individual sites, ADP and occupancies are refined (see 
manual for details which occupancies are in fact refined). For example, 
if you want to include TLS to the list above, then just add a "*" in 
front of corresponding keyword:

strategy = *individual_sites rigid_body *individual_adp group_adp *tls \
               *occupancies group_anomalous

> Sorry for the long list of questions but I am very happy with phenix 
> and just thought I should understand the syntax better.

No problems! Ask as many questions as you need to keep going. Also, you 
may also look at the Manual where there are plenty of examples and 
relevant explanations:
http://www.phenix-online.org/documentation/refinement.htm

Please let me know if you have any other questions,
Pavel.

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