[phenixbb] ADP refinement
PAfonine at lbl.gov
Fri Feb 20 14:52:43 PST 2009
- 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:
phenix.refine model.pdb data.hkl params.txt
where the file "params.txt" contains the following lines:
strategy = *individual_sites rigid_body *individual_adp group_adp *tls \
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
Please let me know if you have any questions!
On 2/20/2009 2:09 PM, Katya Heldwein wrote:
> 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?
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