<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/">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">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>
<br>
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</blockquote></div><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><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org/" style="color:rgb(17,85,204)" target="_blank">https://phenix-online.org</a></div></div></div>