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Hi All, <br>
<br>
just in case somebody else had similar problems: it seems that using
a recent Phenix version 1.13rc1 (2954) fixes the
max_reasonable_bond_distance issue (at least in the reported by Ruki
cases).<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 11/14/17 13:16, Rune Thomas Kidmose
wrote:<br>
</div>
<blockquote type="cite" cite="mid:1510694211865.9257@mbg.au.dk">
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<p>Hi Again Pavel,<br>
</p>
<p><br>
</p>
<p>I should add that this (see download link for PDB file)�is how
the the same PDB file (last_frame.pdb from last email)�looks
when I have put it through phenix.RSR<br>
</p>
<p><br>
</p>
<p>PDB:�<a
href="https://www.dropbox.com/s/ectbydhsh1fx7dh/last_frame_rsr.pdb?dl=0"
moz-do-not-send="true">https://www.dropbox.com/s/ectbydhsh1fx7dh/last_frame_rsr.pdb?dl=0</a><br>
</p>
<p><br>
</p>
<p>The protein part of the model�behaves really well, as I
normally see when using phenix.RSR, however�the DNA seems
to�move much more random, almost uncoiling.<br>
</p>
<p><br>
</p>
<p>This is why I stated that the quality of the refinement seemed
to suffer from the increase max bond distance. B<span
style="font-size: 12pt;">ut again, I am using phenix dev-</span><span
style="font-size: 12pt;">2614 so maybe that has something to
do with it.</span></p>
<p><span style="font-size: 12pt;"><br>
</span></p>
<p><span style="font-size: 12pt;">Cheers</span></p>
<p><span style="font-size: 12pt;">Ruki</span></p>
<p><span style="font-size: 12pt;"><br>
</span></p>
<p><span style="font-size: 12pt;"><br>
</span></p>
<p><br>
</p>
<div style="color: rgb(33, 33, 33);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>Fra:</b> Pavel
Afonine <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a><br>
<b>Sendt:</b> 14. november 2017 16:20<br>
<b>Til:</b> Rune Thomas Kidmose; <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Emne:</b> Re: [phenixbb] Max_reasonble_bond_distance
error in phene.resl.space.refine</font>
<div>�</div>
</div>
<div>Hi Ruki,<br>
<br>
<blockquote type="cite">
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<p>I have been playing around with phenix.real.space.refine
as part of a small pipeline I am making for EM structures.<br>
</p>
<p><br>
</p>
<p>Testing various deposited EM�structures and their
corresponding maps,�within�my pipeline, I sometimes run�in
to the below error:<br>
</p>
<p><br>
</p>
<p>RuntimeError: Bond distance >
max_reasonable_bond_distance: 79.8663 > 50:<br>
</p>
</blockquote>
<br>
I'm trying to chase this down and eliminate. So if you come
across a case that can be reproduced please send it to me and
I will start from there.<br>
<br>
For now simply set "max_reasonable_bond_distance=999" for all
your refinements that will mask but not fix the problem.
However, this should not affect the refinement results.<br>
<br>
Make sure you are using the latest Phenix version.<br>
<br>
<blockquote type="cite">
<p>Followed by a list of distances between, what I am
assuming is, atom numbers and the actual distance.<br>
</p>
<p><br>
</p>
<p>I can get past it simply�by changing
the�max_reasonable_bond_distance�for the run�to, in this
case, 80.<br>
</p>
</blockquote>
<br>
This happens because the procedure optimizes weights by trying
a large sample of possible weight values. For some values
restraints may be too weak and atoms run one onto another,
thus creating a huge clash and strong repulsion that stretches
the bond. This leads to the crash.<br>
<br>
<blockquote type="cite">
<p>But I tend to see, that the final�results gets
significantly�worse when I use this bypass.<br>
</p>
<p>This is based on very similar�models going through the
pipeline, where the ones which yields the error, scores
much worse�when using the above mentioned bypass, compared
to the models that showed no
max_reasonable_distance_error.
<br>
</p>
</blockquote>
<br>
Again, I'm very keep to investigate concrete reproducible
cases. So if you have anything to share that would be most
helpful!<br>
<br>
<blockquote type="cite">
B: Any ide what I can do, to avoid�running�into this bond
distance�problem?<br>
</blockquote>
<br>
I'd say help us to identify the issue so that we fix it and
then you don't run into it any more.<br>
<br>
All the best,<br>
Pavel<br>
<br>
</div>
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</blockquote>
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