[phenixbb] ADP refinement

Pavel Afonine PAfonine at lbl.gov
Fri Feb 20 14:52:43 PST 2009

Hi Katya,

- you can easily do it using phenix.refine GUI (please use the latest 
version of PHENIX for this).

- if you are using the command line version, here is the example that 
illustrates how you can do it...

Essentially, all you need is to specify the tls groups and add tls to 
the strategy (put  "*" in front of "tls"). Here is how:

The command:

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

where the file "params.txt" contains the following lines:

refinement {
 refine {
    strategy = *individual_sites rigid_body *individual_adp group_adp *tls \
               *occupancies group_anomalous
    adp {
      tls = chain A and resseq 123:987
      tls = chain B or chain C
      tls = chain D and resseq 0:100

will refine three TLS groups defined with the above selections in 
addition to the default refinement of individual coordinates for all 
atoms, individual isotropic B-factors for all atoms (including water) 
and occupancies for atoms in alternative conformations of those having 
partial occupancies in input PDB file.

You can create "params.txt" by running this command:

phenix.refine --show-defaults=all > params.txt

and then remove all the keywords that you are not going to modify and 
leave only those that you will be changing.

You can obtain the selections for TLS groups by running your model 
through TLSMD server which creates ready-to-use TLS selections for 
phenix.refine: http://skuld.bmsc.washington.edu/~tlsmd/

Please let me know if you have any questions!


On 2/20/2009 2:09 PM, Katya Heldwein wrote:
> Hi,
> I would like to use TLS refinement for protein (I have selected TLS 
> groups) and individual isotropic refinement for water. How can I specify 
> this in phenix.refine?
> Thanks,
> Katya

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