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<p>Here is the shorter version of Dorothee's example which also
takes care of anisotropic ADPs -- attached.</p>
<p>Pavel<br>
</p>
<div class="moz-cite-prefix">On 6/2/21 01:53, Martin Malý wrote:<br>
</div>
<blockquote type="cite"
cite="mid:f923d942-e213-7695-71fc-b65867d21fac@ibt.cas.cz">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Dear Blaine and Dorothee,<br>
<br>
thank you very much for your thorough responses! It was exactly
what I looked for.<br>
<br>
Best regards,<br>
Martin<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 6/1/21 8:11 PM, Dorothee
Liebschner wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAAA+ObmXmO-swy4mPiR9Ct_wTd_mg6epD8mALhKrnXUD+CdEYA@mail.gmail.com">
<div dir="ltr">Hi Martin,
<div><br>
</div>
<div>You could run the command line tool</div>
<div>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures">phenix.b_factor_statistics
model.pdb</span></p>
</div>
<div>to print information in standard output.</div>
<div><br>
</div>
<div>Or you can use a python script. I wrote a quick example
(attached).</div>
<div>Run it like this:</div>
<div>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures">python
run_average_b.py model.pdb</span></p>
</div>
<div><br>
</div>
<div>Have a look at the cctbx documentation to see some cctbx
example scripts:</div>
<div><a href="http://cci.lbl.gov/docs/cctbx/"
moz-do-not-send="true">http://cci.lbl.gov/docs/cctbx/</a><br>
</div>
<div><br>
</div>
<div>Let us know if you have other questions.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Dorothee</div>
<div> </div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Jun 1, 2021 at 3:21
AM Martin Malý <<a href="mailto:martin.maly@ibt.cas.cz"
moz-do-not-send="true">martin.maly@ibt.cas.cz</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
Dear mailing list members,<br>
<br>
I would like to calculate the mean ADP of a structure model
(PDB) from a<br>
Python script using tools in CCTBX/PHENIX. I tried to find
out how and<br>
dig it from Python source code but I have been unsuccessful
yet. Please,<br>
how to do it (in Python)? Although It is quite easy to
calculate it in<br>
on my own directly from PDB for isotropic ADPs, the
situation can be a<br>
bit complicated for anisotropic ADPs...<br>
<br>
Thank you. Best regards,<br>
Martin Mal<br>
-----<br>
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<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">
<div>Research Scientist, Molecular Biophysics and Integrated
Bioimaging<br>
</div>
<div>Lawrence Berkeley National Laboratory</div>
<div>1 Cyclotron Road, M/S 33R0345</div>
<div>Berkeley, CA 94720</div>
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<p><font size="1">Upozornění: Není-li v této zprávě výslovně
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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. <br>
</font></p>
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nor the acceptance of a proposal to conclude a contract,
nor any other legal act leading to concluding any
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