[phenixbb] Quick calculation of mean ADP

Pavel Afonine pafonine at lbl.gov
Mon Jun 7 12:21:23 PDT 2021


Here is the shorter version of Dorothee's example which also takes care 
of anisotropic ADPs -- attached.

Pavel

On 6/2/21 01:53, Martin Malý wrote:
> Dear Blaine and Dorothee,
>
> thank you very much for your thorough responses! It was exactly what I 
> looked for.
>
> Best regards,
> Martin
>
>
>
> On 6/1/21 8:11 PM, Dorothee Liebschner wrote:
>> Hi Martin,
>>
>> You could run the command line tool
>>
>> phenix.b_factor_statistics model.pdb
>>
>> to print information in standard output.
>>
>> Or you can use a python script. I wrote a quick example (attached).
>> Run it like this:
>>
>> python run_average_b.py model.pdb
>>
>>
>> Have a look at the cctbx documentation to see some cctbx example scripts:
>> http://cci.lbl.gov/docs/cctbx/ <http://cci.lbl.gov/docs/cctbx/>
>>
>> Let us know if you have other questions.
>>
>> Best wishes,
>>
>> Dorothee
>>
>> On Tue, Jun 1, 2021 at 3:21 AM Martin Malý <martin.maly at ibt.cas.cz 
>> <mailto:martin.maly at ibt.cas.cz>> wrote:
>>
>>     Dear mailing list members,
>>
>>     I would like to calculate the mean ADP of a structure model (PDB)
>>     from a
>>     Python script using tools in CCTBX/PHENIX. I tried to find out
>>     how and
>>     dig it from Python source code but I have been unsuccessful yet.
>>     Please,
>>     how to do it (in Python)? Although It is quite easy to calculate
>>     it in
>>     on my own directly from PDB for isotropic ADPs, the situation can
>>     be a
>>     bit complicated for anisotropic ADPs...
>>
>>     Thank you. Best regards,
>>     Martin Mal
>>     -----
>>
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>>     směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní
>>     odpovědnost Biotechnologického ústavu AV ČR, v. v. i.
>>
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>> Lawrence Berkeley National Laboratory
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> -----
>
> Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato 
> e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato 
> zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, 
> v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není 
> návrhem na uzavření smlouvy, ani přijetím případného návrhu na 
> uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření 
> jakékoliv smlouvy a nezakládá předsmluvní odpovědnost 
> Biotechnologického ústavu AV ČR, v. v. i.
>
> Disclaimer: If not expressly stated otherwise, this e-mail message 
> (including any attached files) is intended purely for informational 
> purposes and does not represent a binding agreement on the part of 
> Institute of Biotechnology of the Czech Academy of Sciences. The text 
> of this message and its attachments cannot be considered as a proposal 
> to conclude a contract, nor the acceptance of a proposal to conclude a 
> contract, nor any other legal act leading to concluding any contract, 
> nor does it create any pre-contractual liability on the part of 
> Institute of Biotechnology of the Czech Academy of Sciences.
>
>
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