<div dir="ltr">I just did a git blame and saw you committed the line with "selfUTLIER". This answered one question. Bugs are a different matter.<div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><font face="arial, sans-serif">Cheers</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Nigel</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">---</font></div><div><font face="arial, sans-serif">Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</font></div><div><font face="arial, sans-serif">Lawrence Berkeley National Laboratory</font><br><font face="arial, sans-serif">Berkeley, CA 94720-8235</font><br><font face="arial, sans-serif">Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></font></div></div><div><font face="arial, sans-serif"><span style="color:rgb(73,74,76)">ORCID : </span><font color="#494a4c"><a href="https://orcid.org/0000-0001-8857-9464" target="_blank">orcid.org/0000-0001-8857-9464</a></font></font><br></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 21, 2021 at 8:59 AM Winter, Graeme (DLSLtd,RAL,LSCI) <<a href="mailto:Graeme.Winter@diamond.ac.uk">Graeme.Winter@diamond.ac.uk</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">
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OK, I checked the diffs and it really is just a load of fixing
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<div>function ( args ) :</div>
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<div>type stuff</div>
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<div>Are you sure I made the change here?</div>
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<div>Thanks Graeme<br>
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<div>On 21 Apr 2021, at 16:53, Winter, Graeme (DLSLtd,RAL,LSCI) <<a href="mailto:Graeme.Winter@diamond.ac.uk" target="_blank">Graeme.Winter@diamond.ac.uk</a>> wrote:</div>
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Hi Nigel,
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<div>Search and replace was _probably_ to done as an abstract syntax tree replacement - but I would be surprised if “O” was replaced with “self” (surprised, but not impossible) </div>
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<div>Do you have the commit I could check? Evidently if people did not notice for 2 years the code is not well tested… but equally I am surprised. </div>
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<div>Oh, found it</div>
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<div><a href="https://github.com/cctbx/cctbx_project/commit/c0ac70cab55b41b874bdb2ec1a97d516eb722e42" target="_blank">https://github.com/cctbx/cctbx_project/commit/c0ac70cab55b41b874bdb2ec1a97d516eb722e42</a></div>
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<div>looking...</div>
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<div>Thanks Graeme<br>
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<blockquote type="cite">
<div>On 21 Apr 2021, at 16:48, Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>> wrote:</div>
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Hi,</font><br>
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<div>Not sure if this message was posted earlier or not, that is why I am reposting it.</div>
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<div><font face="arial, sans-serif">I had a couple of questions about sampling backrub and sidechains using the building or refinement modules in cctbx_project/mmtbx.</font></div>
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<div style="margin:0px;font-stretch:normal;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"><font face="arial, sans-serif">1) In the file: <a href="http://mmtbx.building.alternate_conformations.conformer_generation.py/" target="_blank">mmtbx.building.alternate_conformations.conformer_generation.py</a></font></span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"><font face="arial, sans-serif"><br>
</font></span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures">In the function </span><span style="color:rgb(159,160,28);font-variant-ligatures:no-common-ligatures">def</span><span style="font-variant-ligatures:no-common-ligatures"> </span><span style="font-variant-ligatures:no-common-ligatures"><font color="#2eaebb" style="font-weight:bold">__call__: </font><font>the
if statements for checking whether the sampled side chain conformation is a rotamer outlier or not, the check in the if statement is for "selfUTLIER".</font></span></font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures"><br>
</span></font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures"><font>Also in the function </font></span><span style="color:rgb(46,174,187);font-variant-ligatures:no-common-ligatures"><b>set_up_backrub</b></span><span style="font-variant-ligatures:no-common-ligatures">(self):
the atom "O" for the previous residue is not included in the backrun motion, as a result this atom is not moved when the backrub is implemented.</span></font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures"><br>
</span></font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures">I was just wondering if this is a mistake (possibly all instances of "O"
being replaced by "self" which would explain both these things, and some other instances throughout the file), or is this code old and not used anymore?</span></font></div>
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<div>This is exactly the case. It appears that Graeme Winter did a search and replace two years ago. I did a git blame and it shows that the original code was written by Nat Echols 5 years ago. The fact that the code is broken would indicate that the
code is not used or tested well. Feel free to correct it and submit a pull request.</div>
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<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures"><br>
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<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures">2) When trying to run fit_residues.py and tst_fit_residues* scripts in
mmtbx.refinement.real_space, I encountered errors mainly related to chem_data/rotamer_chi_angles/ not being present. Looks like this data is not distributed with cctbx. Is this correct, or maybe there is some other known issue ?</span></font></div>
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<div>You may need the chem_data directory from a Phenix installation.</div>
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<div>Nigel</div>
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<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures">I look forward to hearing from you.</span></font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures"><br>
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<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures">Thanks,</span></font></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures">Swati</span></font></div>
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