<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
Looks great! Thanks Oleg.<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/21/18 12:39, Oleg Sobolev wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CADd3otFVY0zokjEcwzG+_XaUpcSsE5_C8yck6X5gDybHYa4bZA@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<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"
moz-do-not-send="true">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" moz-do-not-send="true">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" moz-do-not-send="true">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"
moz-do-not-send="true">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" moz-do-not-send="true">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909
Web : <a
href="http://CCI.LBL.gov"
target="_blank"
moz-do-not-send="true">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" moz-do-not-send="true">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"
moz-do-not-send="true">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"
moz-do-not-send="true"><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>
<p align="center">To unsubscribe from the
CCTBX-COMMIT list, click the following
link:<br>
<a
href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1"
target="_blank" moz-do-not-send="true">https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1</a>
</p>
</blockquote>
<br>
</div>
_______________________________________________<br>
cctbxbb mailing list<br>
<a href="mailto:cctbxbb@phenix-online.org"
target="_blank" moz-do-not-send="true">cctbxbb@phenix-online.org</a><br>
<a
href="http://phenix-online.org/mailman/listinfo/cctbxbb"
rel="noreferrer" target="_blank"
moz-do-not-send="true">http://phenix-online.org/mailman/listinfo/cctbxbb</a><br>
</blockquote>
</div>
_______________________________________________<br>
cctbxbb mailing list<br>
<a href="mailto:cctbxbb@phenix-online.org"
target="_blank" moz-do-not-send="true">cctbxbb@phenix-online.org</a><br>
<a
href="http://phenix-online.org/mailman/listinfo/cctbxbb"
rel="noreferrer" target="_blank"
moz-do-not-send="true">http://phenix-online.org/mailman/listinfo/cctbxbb</a><br>
</blockquote>
</div>
_______________________________________________<br>
cctbxbb mailing list<br>
<a href="mailto:cctbxbb@phenix-online.org"
target="_blank" moz-do-not-send="true">cctbxbb@phenix-online.org</a><br>
<a
href="http://phenix-online.org/mailman/listinfo/cctbxbb"
rel="noreferrer" target="_blank"
moz-do-not-send="true">http://phenix-online.org/mailman/listinfo/cctbxbb</a><br>
</blockquote>
</div>
<br>
<fieldset
class="gmail-m_-7842798474965407074mimeAttachmentHeader"></fieldset>
<br>
<pre>_______________________________________________
cctbxbb mailing list
<a class="gmail-m_-7842798474965407074moz-txt-link-abbreviated" href="mailto:cctbxbb@phenix-online.org" target="_blank" moz-do-not-send="true">cctbxbb@phenix-online.org</a>
<a class="gmail-m_-7842798474965407074moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/cctbxbb" target="_blank" moz-do-not-send="true">http://phenix-online.org/mailman/listinfo/cctbxbb</a>
</pre>
</blockquote>
<br>
</div>
</blockquote>
</div>
</blockquote>
<br>
</body>
</html>