<div dir="ltr"><div dir="ltr"><br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><font color="#000000" face="arial, sans-serif">Hi,</font><br><div style="color:rgb(0,0,0)"><br></div><div style="color:rgb(0,0,0)">Not sure if this message was posted earlier or not, that is why I am reposting it.</div><div style="color:rgb(0,0,0)"><br></div><div style="color:rgb(0,0,0)"><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><div style="color:rgb(0,0,0)"><font face="arial, sans-serif"><br></font></div><div style="color:rgb(0,0,0)"><p 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></p><p 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></p><p 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 color="#000000">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></p><p 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></p><p style="margin:0px;font-stretch:normal;line-height:normal"><font face="arial, sans-serif"><span style="font-variant-ligatures:no-common-ligatures"><font color="#000000">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></p><p 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></p><p 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></p></div></div></div></blockquote><div><br></div><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><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div style="color:rgb(0,0,0)"><p 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></p><p 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></p></div></div></div></blockquote><div><br></div><div>You may need the chem_data directory from a Phenix installation.</div><div><br></div><div>Nigel</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div style="color:rgb(0,0,0)"><p 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></p><p 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></p><p 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></p><p 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></p><p 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></p></div></div></div>
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