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 ...

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 :-) ).
I think its best to either set the origin of the box so that no coordinates or  restraints have to move or be removed.
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.

Best,
Gydo

On Fri, Dec 21, 2018 at 11:59 AM Nigel Moriarty <nwmoriarty@lbl.gov> wrote:
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. 

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Thu, Dec 20, 2018 at 5:02 PM Pavel Afonine <pafonine@lbl.gov> wrote:
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.

Pavel

On 12/20/18 09:53, CCTBX commit wrote:
Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx
On branch  : master



commit 1ad3fe05571162839e770c35ed032a7fc38a33b7
Author: Gydo van Zundert <gydo.vanzundert@schrodinger.com>
Date:   Wed Dec 19 14:58:36 2018 -0500

    Fix typo geobox




1ad3fe05571162839e770c35ed032a7fc38a33b7
mmtbx/refinement/real_space/individual_sites.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mmtbx/refinement/real_space/individual_sites.py b/mmtbx/refinement/real_space/individual_sites.py
index c61e88b01..20f38a6b0 100644
--- a/mmtbx/refinement/real_space/individual_sites.py
+++ b/mmtbx/refinement/real_space/individual_sites.py
@@ -350,7 +350,7 @@ class box_refinement_manager(object):

       # When using the Schrodinger force field, move the whole structure as the
       # selected atoms are environment aware.
-      if geobox.get_source() == 'SCHRODINGER':
+      if geo_box.get_source() == 'SCHRODINGER':
         geo_box.shift_cart(box.shift_cart)

       rsr_simple_refiner = simple(
@@ -377,7 +377,7 @@ class box_refinement_manager(object):
         iselection, sites_cart_refined)
       self.xray_structure.set_sites_cart(sites_cart_moving)
       self.sites_cart = self.xray_structure.sites_cart()
-      if geobox.get_source() == 'SCHRODINGER':
+      if geo_box.get_source() == 'SCHRODINGER':
         geo_box.shift_cart(shift_back)
     else: # NCS constraints are present
       # select on xrs, grm, ncs_groups

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