[phenixbb] Obtaining just the Wilson B with Xtriage
mortengroftehauge.work at gmail.com
Wed Mar 26 10:11:48 PDT 2014
Thank you to Pavel, Robbie and Mark og tak til Bjørn og Robert.
It was the last day of this student's project and she was doing some kind
of coarse-grain protein dynamics model. This was the first time she asked
me for help so I had to both (try) to understand what she was doing and
figure out how to help her in the quickest manner while introducing the
fewest new pieces of software. And I was a bit tired *ahem* from the going
away party the night before.
Robbie's solution was by far the easiest. Basically, he has a list of all
the Wilson B-factors for experimental data in the pdb from his work on
PDB_REDO. It's a long list.
This gave her more consistent data when analysing the experimental
structures. I don't know if it measurably influenced the model results.
The lesson is of course that if you are going to analyse data deposited by
other people... Blah, blah. Starting over.
If you analyse x-ray crystal structures and you aren't a crystallographer
then you should go ally yourself with one from the beginning.
Thanks for all the help and suggestions guys.
On 21 March 2014 18:55, Pavel Afonine <pafonine at lbl.gov> wrote:
> Sounds like Phenix is missing a command line tool as simple as this:
> phenix.wilson_b data.mtz label="F-obs"
> On 3/21/14, 11:42 AM, R.D. Oeffner wrote:
>> From phenix.python you can script it like:
>> Python 2.7.3 (default, Apr 10 2012, 23:24:47) [MSC v.1500 64 bit (AMD64)]
>> on win32
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> from mmtbx.scaling import xtriage
>>>>> xtrobj = xtriage.run(["dom2.1.mtz", "--quiet"])
>>>>> print "Wilson B= %2.2f" %xtrobj.basic_results.iso_b_wilson
>>>> Wilson B= 161.98
>> The script will then only print the B factor although xtriage still does
>> "everything else" under the hood.
>> On 2014-03-21 16:45, Morten Grøftehauge wrote:
>>> Hi guys,
>>> Is there a way to just have phenix.xtriage compute and output the
>>> Wilson B factor and not do everything else? I want to run it on a lot
>>> of files and that would simplify things.
>>> Morten K Grøftehauge, PhD
>>> Pohl Group
>>> Durham University
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>> phenixbb mailing list
>> phenixbb at phenix-online.org
Morten K Grøftehauge, PhD
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