<div dir="ltr"><div dir="ltr">Hi Pavel, Gydo,<div><br></div><div>Here it is:</div><div><a href="https://github.com/cctbx/cctbx_project/commit/cc21afcf004aedfcfc71bc16d06738abf441c085">https://github.com/cctbx/cctbx_project/commit/cc21afcf004aedfcfc71bc16d06738abf441c085</a><br></div><div><br></div><div>Gydo, please note slightly different function name and correct you code accordingly.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev. </div></div></div><br><div class="gmail_quote"><div dir="ltr">On Fri, Dec 21, 2018 at 10:45 AM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<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 bgcolor="#FFFFFF">
Hi Oleg,<br>
<br>
I did not follow this conversation, so I don't know details and
nuances. All I care about is making sure we don't have lines like<br>
<br>
if geo_box.get_source() == 'SCHRODINGER':<br>
<br>
in low-level codes (for reasons I hinted earlier). So if that gets
removed one way or another I'm happy!<br>
<br>
All the best,<br>
Pavel<br>
<br>
<div class="gmail-m_-7842798474965407074moz-cite-prefix">On 12/21/18 10:36, Oleg Sobolev wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">Hi Pavel, Gydo,
<div><br>
</div>
<div>I agree with Gydo's points. The best way forward would
be to implement shift_cart() function for base geometry
and actually treat reference coordinate restraints
appropriately even in our basic GRM instead of throwing
them away and getting biased estimation of weight.</div>
<div><br>
</div>
<div>Secondly, we can remove the second call </div>
<div>
<div> if geo_box.get_source() == 'SCHRODINGER':</div>
<div> geo_box.shift_cart(shift_back)</div>
</div>
<div>completely right now, because we throw away geo_box and
don't need to care about shifting stuff back.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
<div><br>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Fri, Dec 21, 2018 at 9:37 AM Gydo van Zundert
<<a href="mailto:gydo.vanzundert@schrodinger.com" target="_blank">gydo.vanzundert@schrodinger.com</a>>
wrote:<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>Thanks for the feedback Pavel. First off, let me start
by saying I'm feeling hesitant about sharing what I think
is best, since I'm obviously an outsider and you guys are
the keepers of the code. Anyway ...<br>
</div>
<div><br>
</div>
<div>I agree that checking whether the geometry restraints
manager is using Schrodinger restraints is not elegant and
ideally should be removed. The issue here is that a part
of the map is being boxed out corresponding to a chunk of
the chain. However, this newly created box has its origin
set to (0, 0, 0), which means that the chunk also needs to
move accordingly if it is to stay in the same relative
position of the density. This boxing behavior is leading
to some quircks even in the original code, since it
requires that the reference_coordinate restraints are
removed from the geometry_restraints_manager during the
weight determination of the chunk and the density (else
"disaster" happens according to a comment :-) ).<br>
</div>
<div>I think its best to either set the origin of the box so
that no coordinates or restraints have to move or be
removed. <br>
</div>
<div>It also got me wondering why the density is being boxed
out, is there a (performance) reason for this being done?
Since typically only the values under the atom coordinates
or its surroundings are used, it should not really matter
on the size of the map, since you can efficiently loop
over the relevant voxels or do linear interpolation on the
atom positions, something which you do anyway. You might
even get a marginal performance increase, since some
operations can be removed, by just using the original
larger map.<br>
</div>
<div><br>
</div>
<div>Best,</div>
<div>Gydo<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Fri, Dec 21, 2018 at 11:59 AM Nigel
Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>>
wrote:<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">Not sure if Gydo is seeing this but it may
be outside his expertise. To me. it highlights a wrinkle
in the code. The only reason for not shifting is so that
the forcefields are consistent in the long range terms.
I believe it could be avoided by moving the entire model
such that the submodel is in the required position but
the other atoms are in the correct relative position.
<div><br clear="all">
<div>
<div dir="ltr" class="gmail-m_-7842798474965407074gmail-m_6035888157603407385gmail-m_5003749320834457516gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">Cheers
<div><br>
</div>
<div>Nigel
<div><br>
</div>
<div>---</div>
<div>Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics
and Integrated Bioimaging</div>
<div>Lawrence Berkeley National
Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email :
<a class="gmail-m_-7842798474965407074moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov" target="_blank">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Thu, Dec 20, 2018 at 5:02 PM Pavel
Afonine <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>>
wrote:<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 bgcolor="#FFFFFF"> Bad idea to hard-wire package
name into lowest level code. Now imagine we need the
same for afit, amber, quantumbio, rosetta, etc.. Are
we going to have a page-long block of "if"
statements. Please re-think and remove. For example,
whether you want to shift it or not can be a
parameter that you cast way level up in the context
specific code.<br>
<br>
Pavel<br>
<br>
<div class="gmail-m_-7842798474965407074gmail-m_6035888157603407385gmail-m_5003749320834457516gmail-m_8321930562097640801moz-cite-prefix">On
12/20/18 09:53, CCTBX commit wrote:<br>
</div>
<blockquote type="cite"> <tt>Repository : <a class="gmail-m_-7842798474965407074gmail-m_6035888157603407385gmail-m_5003749320834457516gmail-m_8321930562097640801moz-txt-link-freetext">ssh://g18-sc-serv-04.diamond.ac.uk/cctbx</a><br>
On branch : master<br>
<br>
<hr><br>
<br>
commit 1ad3fe05571162839e770c35ed032a7fc38a33b7<br>
Author: Gydo van Zundert <a class="gmail-m_-7842798474965407074gmail-m_6035888157603407385gmail-m_5003749320834457516gmail-m_8321930562097640801moz-txt-link-rfc2396E" href="mailto:gydo.vanzundert@schrodinger.com" target="_blank"><gydo.vanzundert@schrodinger.com></a><br>
Date: Wed Dec 19 14:58:36 2018 -0500<br>
<br>
Fix typo geobox<br>
<br>
<br>
<hr><br>
<br>
1ad3fe05571162839e770c35ed032a7fc38a33b7<br>
mmtbx/refinement/real_space/individual_sites.py
| 4 ++--<br>
1 file changed, 2 insertions(+), 2 deletions(-)<br>
<br>
diff --git
a/mmtbx/refinement/real_space/individual_sites.py
b/mmtbx/refinement/real_space/individual_sites.py<br>
index c61e88b01..20f38a6b0 100644<br>
<tt style="color:rgb(136,0,0)">---
a/mmtbx/refinement/real_space/individual_sites.py</tt><br>
<tt style="color:rgb(0,0,136)">+++
b/mmtbx/refinement/real_space/individual_sites.py</tt><br>
@@ -350,7 +350,7 @@ class
box_refinement_manager(object):<br>
<br>
# When using the Schrodinger force field,
move the whole structure as the<br>
# selected atoms are environment aware.<br>
<tt style="color:rgb(136,0,0)">- if
geobox.get_source() == 'SCHRODINGER':</tt><br>
<tt style="color:rgb(0,0,136)">+ if
geo_box.get_source() == 'SCHRODINGER':</tt><br>
geo_box.shift_cart(box.shift_cart)<br>
<br>
rsr_simple_refiner = simple(<br>
@@ -377,7 +377,7 @@ class
box_refinement_manager(object):<br>
iselection, sites_cart_refined)<br>
self.xray_structure.set_sites_cart(sites_cart_moving)<br>
self.sites_cart =
self.xray_structure.sites_cart()<br>
<tt style="color:rgb(136,0,0)">- if
geobox.get_source() == 'SCHRODINGER':</tt><br>
<tt style="color:rgb(0,0,136)">+ if
geo_box.get_source() == 'SCHRODINGER':</tt><br>
geo_box.shift_cart(shift_back)<br>
else: # NCS constraints are present<br>
# select on xrs, grm, ncs_groups<br>
</tt> <br>
<hr>
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