<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">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_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 : NWMoriarty@LBL.gov<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_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_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_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>
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