selected_atoms not current

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.dev202103310726 (2021-03-31 07:26:37 UTC)
Description
Some change since ChimeraX 1.1 has broken a few methods in ISOLDE (including some *very* old code) in a strange way. For example, when I try to start a simulation with atoms from more than one model selected (worked in ChimeraX 1.1, fails now with unchanged code). The culprit appears to be the `Isolde._get_main_sim_selection()` method at https://github.com/tristanic/isolde/blob/3bafd1bc006f9a7054938c270fba6387a918ae6d/isolde/src/isolde.py#L2918, which aggregates the atoms to keep/exclude by changing their `selected` property (I realise this could probably be done more neatly - but as I said, this is very old code from the early days of ISOLDE). At the start of the method it sets `selected=False` for all currently-selected atoms and re-sets it to True only for those atoms that are part of ISOLDE's currently-selected model. It then does some logic to expand the selection back and forth along each chain, and finally returns `selected_atoms(session)`. The problem that's new since ChimeraX 1.1 is that `selected_atoms(session)` still includes *all* atoms that were selected at the time `_get_main_sim_selection()` was called, including those for which `selected` has since been set to False. I can get around it easily enough, but the behaviour seems non-ideal. 

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

UCSF ChimeraX version: 1.2.dev202103310726 (2021-03-31)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> open 3io0 structureFactors true

Summary of feedback from opening 3io0 fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Resolution: 3.003  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 28,28,26, pixel 0.963, shown at
level 0.283, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 28,28,26, pixel 0.963, shown at
level -0.057,0.057, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 28,28,26, pixel 0.963,
shown at level 0.565, step 1, values float32  
3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0  
---  
Chain | Description  
1.2/A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 28,28,26, pixel 0.963,
shown at level 0.339, step 1, values float32  

> open 3io0

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #2  
---  
Chain | Description  
A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | Termini for 3io0 (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 3io0 #1.2/A PRO 76  
Chain-final residues that are actual C termini: 3io0 #1.2/A PHE 304  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue 3io0 #1.2/A PHE 304  
198 hydrogen bonds  
Termini for 3io0 (#2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 3io0 #2/A PRO 76  
Chain-final residues that are actual C termini: 3io0 #2/A PHE 304  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue 3io0 #2/A PHE 304  
198 hydrogen bonds  
3384 hydrogens added  
  

> select #1,2

6702 atoms, 6746 bonds, 460 residues, 25 models selected  
Updating bulk solvent parameters...  
Traceback (most recent call last):  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2719, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2753, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 576, in __init__  
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 968, in
expand_mobile_selection  
sel = selections.expand_selection_along_chains(core_atoms,  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/selections.py", line 40, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
TypeError: Selected atoms must all be in the same model!  
  
TypeError: Selected atoms must all be in the same model!  
  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/selections.py", line 40, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
  
See log for complete Python traceback.  
  

> ui tool show Shell

/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select #1,2

6702 atoms, 6746 bonds, 460 residues, 25 models selected  




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OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
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	Kernel driver in use: nvidia
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[Eric Pettersen]

Hi Tristan,

This is undoubtedly due to some newish code that tracks the order in which atoms are selected and returns them in that order. I *think* I know what the problem is. Will try to get to it today.

--Eric

[Eric Pettersen]

Hi Tristan,

Could you check that this change fixes your problem (and doesn't blow anything else up)? Thanks!

--Eric

diff --git a/src/bundles/atomic/src/changes.py b/src/bundles/atomic/src/changes.py
index 92b618f33..418f7ca4a 100644
--- a/src/bundles/atomic/src/changes.py
+++ b/src/bundles/atomic/src/changes.py
@@ -177,6 +177,7 @@ class Changes:

def selected_atoms(session=None):

global _full_sel, _ordered_sel

+ check_for_changes(session)

from .molarray import Atoms
return _ordered_sel if _ordered_sel is not None else (_full_sel if _full_sel is not None else Atoms())

[Tristan Croll]

Very tied up with some urgent work right now, but will do as soon as possible. Although, my bigger problem with that particular code was that using selected_atoms(session)​ was a silly way of doing things, when I could just do m.atoms[m.atoms.selecteds]​ and avoid any ambiguity while also being slightly more efficient...
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 26 April 2021 20:06
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4560: selected_atoms not current

#4560: selected_atoms not current
------------------------------------+----------------------------
          Reporter:  Tristan Croll  |      Owner:  Eric Pettersen
              Type:  defect         |     Status:  feedback
          Priority:  normal         |  Milestone:
         Component:  Core           |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback


Comment:

 Hi Tristan,
         Could you check that this change fixes your problem (and doesn't
 blow anything else up)?  Thanks!

 --Eric

 diff --git a/src/bundles/atomic/src/changes.py
 b/src/bundles/atomic/src/changes.py
 index 92b618f33..418f7ca4a 100644
 --- a/src/bundles/atomic/src/changes.py
 +++ b/src/bundles/atomic/src/changes.py
 @@ -177,6 +177,7 @@ class Changes:

  def selected_atoms(session=None):
      global _full_sel, _ordered_sel
 +    check_for_changes(session)
      from .molarray import Atoms
      return _ordered_sel if _ordered_sel is not None else (_full_sel if
 _full_sel is not None else Atoms())

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4560#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Sure. I guess I'll commit the change for now so it gets into the 1.2 release candidate, but will back it out if your testing uncovers deleterious effects.

--Eric

[Eric Pettersen]

I guess I'll assume it worked. Feel free to reopen if it's still a problem.

[Tristan Croll]

Sorry for not following up. All seems to behave correctly now.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 09 June 2021 02:03
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4560: selected_atoms not current

#4560: selected_atoms not current
------------------------------------+----------------------------
          Reporter:  Tristan Croll  |      Owner:  Eric Pettersen
              Type:  defect         |     Status:  closed
          Priority:  normal         |  Milestone:
         Component:  Core           |    Version:
        Resolution:  fixed          |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  feedback => closed
 * resolution:   => fixed


Comment:

 I guess I'll assume it worked.  Feel free to reopen if it's still a
 problem.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4560#comment:5>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Good to hear!

--Eric