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<p>Hi Swati,</p>
<p>a possible (and perhaps the best!) way to know that your
installation works as intended is to run tests (tst*.py files)
located in <br>
</p>
<p>cctbx_project/mmtbx/refinement/real_space</p>
<p>If they pass then all is good (for the code these tests are
exercising, of course)!</p>
<p>Good Luck,<br>
Pavel<br>
</p>
<div class="moz-cite-prefix">On 4/22/21 02:13, Swati Jain wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CADaZETgyA-iz_QeGqsb0chdpRSvrtJcdZs4MwOj2=R9KD1EWGw@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi everyone,
<div><br>
</div>
<div>Thanks a lot for the information. Seems like you all agree
that this code is old and not tested.</div>
<div><br>
</div>
<div>Regarding the chem_data question, I don't have a phenix
license. I was able to get some chem_data information (geostd
from sourceforge and mon_lib and rama and rota evaluation
information from the Richardson lab), but not the directory
that is needed for the fit_residue* functions. </div>
<div><br>
</div>
<div>However, the individual_sites real space refinement seems
to be working fine, both the test script as well as when I try
it myself. Am I correct is assuming that it does not require
any additional data (apart from the openly available data I
was able to get) or the code is not throwing any errors and
just skipping steps?</div>
<div><br>
</div>
<div>Thanks a lot,</div>
<div>Swati</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Apr 21, 2021 at 9:18
PM Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov"
moz-do-not-send="true">nwmoriarty@lbl.gov</a>> wrote:<br>
</div>
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<div dir="ltr">
<div dir="ltr"><br>
</div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px
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<div dir="ltr">
<div dir="ltr"><font face="arial, sans-serif"
color="#000000">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" moz-do-not-send="true">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
style="font-weight:bold" color="#2eaebb">__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-width:1px;border-left-style:solid;border-left-color: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-width:1px;border-left-style:solid;border-left-color: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>
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