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OK, I checked the diffs and it really is just a load of fixing
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<div class="">Are you sure I made the change here?</div>
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<div class="">Thanks Graeme<br class="">
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<div class="">On 21 Apr 2021, at 16:53, Winter, Graeme (DLSLtd,RAL,LSCI) <<a href="mailto:Graeme.Winter@diamond.ac.uk" class="">Graeme.Winter@diamond.ac.uk</a>> wrote:</div>
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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 style="" class="">Not sure if this message was posted earlier or not, that is why I am reposting it.</div>
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<div style="" class=""><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 style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><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 style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">In the function </span><span style="color: rgb(159, 160, 28); font-variant-ligatures: no-common-ligatures;" class="">def</span><span style="font-variant-ligatures: no-common-ligatures;" class=""> </span><span style="font-variant-ligatures: no-common-ligatures;" class=""><font color="#2eaebb" style="font-weight: bold;" class="">__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 style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font class="">Also in the function </font></span><span style="color: rgb(46, 174, 187); font-variant-ligatures: no-common-ligatures;" class=""><b class="">set_up_backrub</b></span><span style="font-variant-ligatures: no-common-ligatures;" class="">(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>
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</span></font></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">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 style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">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 style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">I look forward to hearing from you.</span></font></div>
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">Thanks,</span></font></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><font face="arial, sans-serif" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">Swati</span></font></div>
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