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Thank you Pavel for the m.pdb file. I did the dynamics run. What
am I looking for? I still see adjacent CA-CA distances all below
3.8 A. The other three minimizers give me all CA-CA > 3.85 A.<br>
<br>
Maybe I am missing your point?<br>
<br>
<br>
<div class="moz-cite-prefix">On 7/8/2021 11:29 AM, Pavel Afonine
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:d2167510-c3ca-e78f-1dd8-6259ce44a5a2@lbl.gov">
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<p>Hi James,<br>
</p>
<blockquote type="cite"
cite="mid:192cf406-b24c-27d6-a315-942087d052ef@lbl.gov">
<blockquote type="cite"
cite="mid:c408af9f-5623-e5d1-c25b-231ef5f724b5@lbl.gov">
<blockquote type="cite">Greetings all, and I hope this little
observation helps improve things somehow. <br>
<br>
I did not expect this result, but there it is. My MolProbity
score goes from 0.7 to 1.9 after a run of
phenix.geometry_minimization <br>
<br>
I started with an AMBER-minimized model (based on 1aho), and
that got me my best MolProbity score so far (0.7). But, even
with hydrogens and waters removed the geometry_minimization
run increases the clashscore from 0 to 3.1 and Ramachandran
favored drops from 98% to 88% with one residue reaching the
outlier level. <br>
</blockquote>
<br>
It is not a secret that 'standard geometry restraints' used in
Phenix and alike (read Refmac, etc) are very simplistic. They
are not aware of main chain preferential conformations
(Ramachandran plot), favorable side chain rotamer
conformations. They don't even have any
electrostatic/attraction terms -- only anti-bumping repulsion!
Standard geometry restraints won't like any NCI (non-covalent
interaction) and likely will make interacting atoms break
apart rather than stay close together interacting. <br>
</blockquote>
<br>
Yes, there's the rub: I'm not seeing "interacting atoms break
apart", but rather they are being smashed together. Torsion
angles are also being twisted out of allowed regions of the
Ramachandran plot. <br>
</blockquote>
<p>I think this can go both ways depending on local arrangement.
For example, if atoms interact via NCI but something else pushes
them apart, they will split. But if nothing pushes them they may
just stay together.<br>
</p>
<p>Also, if H are not present atoms can come close enough to
each-other creating a clash from MolProbity viewpoint (because
it adds H for clash evaluations).<br>
</p>
<blockquote type="cite"
cite="mid:192cf406-b24c-27d6-a315-942087d052ef@lbl.gov">
<blockquote type="cite"
cite="mid:c408af9f-5623-e5d1-c25b-231ef5f724b5@lbl.gov">With
this in mind any high quality (high-resolution) atomic model
or the one optimized using sufficiently high-level QM is going
to have a more realistic geometry than the result of geometry
regularization against very simplistic restraints target. An
example: <br>
<br>
<a class="moz-txt-link-freetext"
href="https://journals.iucr.org/d/issues/2020/12/00/lp5048/lp5048.pdf"
moz-do-not-send="true">https://journals.iucr.org/d/issues/2020/12/00/lp5048/lp5048.pdf</a>
<br>
<br>
and previous papers on the topic. <br>
</blockquote>
<br>
I agree, but what doesn't make sense to me is how the
"simplistic restraints" of phenix.geometry_minimization would be
so inconsistent with the "simplistic restraints" in
phenix.molprobity ?<br>
</blockquote>
<br>
MolProbity way to quantify clashes and repulsion terms in standard
restraints are different. If everything else is favorable they may
match, but otherwise they don't have to (by the way they are
defined and calculated).<br>
<br>
<blockquote type="cite"
cite="mid:192cf406-b24c-27d6-a315-942087d052ef@lbl.gov"> What I
am doing here is starting with an energy-minimized model of a
1.0 A structure (1aho). It's not a fancy QM, just the ff14SB
potential in AMBER. I get my best molprobity scores this way,
but I need an x-ray refinement program like phenix.refine to
compare these models with reality. It troubles me that the
"geometry" in the x-ray refinement program all by itself messes
up my molprobity score.<br>
</blockquote>
<br>
If in this case AMBER force-field does a better job, then you can
run X-ray refinement using AMBER based restraints. Nigel can help
with that in case it does not work right off the box.<br>
<br>
<blockquote type="cite"
cite="mid:192cf406-b24c-27d6-a315-942087d052ef@lbl.gov">
<blockquote type="cite"
cite="mid:c408af9f-5623-e5d1-c25b-231ef5f724b5@lbl.gov">
<blockquote type="cite">Just for comparison, with refmac5 in
"refi type ideal" mode I see the MolProbity rise to 1.13,
but Clashscore remains zero, some Ramas go from favored to
allowed, but none rise to the level of outliers. <br>
</blockquote>
<br>
I believe this is because of the nature of minimizer used.
Refmac uses 2nd derivative based one, which in a nutshell
means it can move the model much less (just a bit in vicinity
of a local minimum) than any program that uses gradients only
(like Phenix). <br>
</blockquote>
good point.<br>
<br>
So, what should I do to stabilize phenix.geometry_minimization?
Crank up the non-bonded weight? Restrain to starting
coordinates?<br>
</blockquote>
<br>
Restraining to starting coordinates is a fine option (there is an
option to do it).
<p>Cranking up nonbonded weight might have side effects:</p>
<p><a class="moz-txt-link-freetext"
href="http://phenix-online.org/presentations/nb_weight.pdf"
moz-do-not-send="true">http://phenix-online.org/presentations/nb_weight.pdf</a><br>
</p>
<blockquote type="cite"
cite="mid:192cf406-b24c-27d6-a315-942087d052ef@lbl.gov">
<blockquote type="cite"
cite="mid:c408af9f-5623-e5d1-c25b-231ef5f724b5@lbl.gov">
<blockquote type="cite">Files and logs here: <br>
<a class="moz-txt-link-freetext"
href="https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz"
moz-do-not-send="true">https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz</a>
<br>
<br>
I suspect this might have something to do with library
values for main-chain bonds and angles? They do seem to
vary between programs. Phenix having the shortest CA-CA
distance by up to 0.08 A. After running thorough
minimization on a poly-A peptide I get: <br>
bond amber refmac phenix shelxl Stryer <br>
C-N 1.330 1.339 1.331 1.325 1.32 <br>
N-CA 1.462 1.482 1.455 1.454 1.47 <br>
CA-C 1.542 1.534 1.521 1.546 1.53 <br>
CA-CA 3.862 3.874 <font color="#ff0000"><b>3.794</b></font>
3.854 <br>
<br>
So, which one is "right" ? <br>
</blockquote>
<br>
I'd say they are all the same, within their 'sigmas' which are
from memory about 0.02A: <br>
</blockquote>
I note that 3.874 - 3.794 = 0.08 > 0.02<br>
</blockquote>
<br>
Right, but I was talking about covalent bonds as defined in
Monomer Library or GeoStd, and for those it looks like they stay
within their 'sigmas'. There is no explicit restraints on CA-CA
distances.<br>
<br>
<blockquote type="cite"
cite="mid:192cf406-b24c-27d6-a315-942087d052ef@lbl.gov"> This
brings me to my pet theory. I think what is going on is small
errors like this build up a considerable amount of tension in
the long main chain. For this 64-mer, the contour length of the
main chain after idealization is ~5 A shorter after
phenix.geometry_minimization than it is after shelxl or amber.
That 5 A has to come from somewhere. Without stretching bonds
or bending angles the only thing left to do is twisting
torsions. A kind of "whirlygig" effect.<br>
<br>
The question is: is the phenix CA-CA distance too short? Or is
the amber CA-CA distance too long?<br>
</blockquote>
<p>I don't know the answer, but try this (m.pdb is a nearly
perfect alpha-helix from 1US0):</p>
<p>phenix.dynamics m.pdb number_of_steps=5000</p>
<p>and compare the result (eg., in PyMol) with the staring model.</p>
<p>Pavel</p>
<p><br>
</p>
<br>
</blockquote>
<br>
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