Hi Ursula,
here is a solution, not nice though:
step 1: get a pdb file with chain in question:
phenix.pdbtools model.pdb keep="chain A"
output.file_name="chain_A.pdb"
step 2: then this will give you average B
phenix.pdbtools chain_A.pdb model_statistics=true
Other suggestions (by David & Christian) might work too, but I
have no idea how these programs handle TLS contribution to ADP and
ANISOU records. Though since phenix.refine outputs total ADPs I
guess this should be just fine.
Pavel
On 7/12/12 9:24 AM, Ursula Schulze-Gahmen wrote:
Hi Pavel,
Yes, I see the baverage in the header of the pdb file. But I would
like to get the baverage for the different chains in the
structure. I tried using "phenix.pdbtools model.pdb
model_statistics=true" on separate chains, but I don't get a value
for Baverage from this.
Ursula
On Wed, Jul 11, 2012 at 11:58 AM, Pavel
Afonine
<[email protected]>
wrote:
Hi Ursula,
Is there an easy way to calculate average temperature
factors in phenix or another program after ADP + TLS
refinement in phenix?
yes. If you PDB file is after phenix.refine run, then the
average ADP is reported in PDB file header as well as in
refinement log file.
For a PDB file you can calculate average ADP using this
command:
phenix.pdbtools model.pdb model_statistics=true
It does not matter where PDB file come from as long as ATOM
or/and ANISOU records contain the correct ADPs.
Pavel
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Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220
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