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The bug was present in the original implementation of the code:</div>
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<a href="https://github.com/cctbx/cctbx_project/commit/13b9b26f622fe8a99cc65102b657f551ab1ecb33#diff-7299f5e6607d26db001fa97199b85100bd388c682f736db5a49029ea2cbe3ad0R403">https://github.com/cctbx/cctbx_project/commit/13b9b26f622fe8a99cc65102b657f551ab1ecb33#diff-7299f5e6607d26db001fa97199b85100bd388c682f736db5a49029ea2cbe3ad0R403</a><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> cctbxbb-bounces@phenix-online.org <cctbxbb-bounces@phenix-online.org> on behalf of Winter, Graeme (DLSLtd,RAL,LSCI) <Graeme.Winter@diamond.ac.uk><br>
<b>Sent:</b> 21 April 2021 16:53<br>
<b>To:</b> cctbx mailing list <cctbxbb@phenix-online.org><br>
<b>Subject:</b> Re: [cctbxbb] Question/a possible typo in sampling backrub and side chain conformations in mmtbx</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Nigel,
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<div class="">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 class="">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 class="">Oh, found it</div>
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<div class=""><a href="https://github.com/cctbx/cctbx_project/commit/c0ac70cab55b41b874bdb2ec1a97d516eb722e42" class="">https://github.com/cctbx/cctbx_project/commit/c0ac70cab55b41b874bdb2ec1a97d516eb722e42</a></div>
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<div class="">looking...</div>
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<div class="">Thanks Graeme<br class="">
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<div class="">On 21 Apr 2021, at 16:48, Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" class="">nwmoriarty@lbl.gov</a>> wrote:</div>
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Hi,</font><br class="">
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<div class="" style="">Not sure if this message was posted earlier or not, that is why I am reposting it.</div>
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<div class="" style=""><font face="arial, sans-serif" class="">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 class="" style="margin:0px; font-stretch:normal; line-height:normal"><span class="" style="font-variant-ligatures:no-common-ligatures"><font face="arial, sans-serif" class="">1) In the file: <a href="http://mmtbx.building.alternate_conformations.conformer_generation.py/" target="_blank" class="">mmtbx.building.alternate_conformations.conformer_generation.py</a></font></span></div>
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</font></span></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal"><font face="arial, sans-serif" class=""><span class="" style="font-variant-ligatures:no-common-ligatures">In the function </span><span class="" style="color:rgb(159,160,28); font-variant-ligatures:no-common-ligatures">def</span><span class="" style="font-variant-ligatures:no-common-ligatures"> </span><span class="" style="font-variant-ligatures:no-common-ligatures"><font color="#2eaebb" class="" style="font-weight:bold">__call__: </font><font class="">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>
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</span></font></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal"><font face="arial, sans-serif" class=""><span class="" style="font-variant-ligatures:no-common-ligatures"><font class="">Also in the function </font></span><span class="" style="color:rgb(46,174,187); font-variant-ligatures:no-common-ligatures"><b class="">set_up_backrub</b></span><span class="" 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 class="" style="margin:0px; font-stretch:normal; line-height:normal"><font face="arial, sans-serif" class=""><span class="" style="font-variant-ligatures:no-common-ligatures"><br class="">
</span></font></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal"><font face="arial, sans-serif" class=""><span class="" 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 class="">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 class="" style="margin:0px; font-stretch:normal; line-height:normal"><font face="arial, sans-serif" class=""><span class="" 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 class="">You may need the chem_data directory from a Phenix installation.</div>
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<div class="">Nigel</div>
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<div class="" style="margin:0px; font-stretch:normal; line-height:normal"><font face="arial, sans-serif" class=""><span class="" style="font-variant-ligatures:no-common-ligatures">I look forward to hearing from you.</span></font></div>
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<div class="" style="margin:0px; font-stretch:normal; line-height:normal"><font face="arial, sans-serif" class=""><span class="" style="font-variant-ligatures:no-common-ligatures">Thanks,</span></font></div>
<div class="" style="margin:0px; font-stretch:normal; line-height:normal"><font face="arial, sans-serif" class=""><span class="" style="font-variant-ligatures:no-common-ligatures">Swati</span></font></div>
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