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 and this
one .
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.