id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2589	Basic Clipper session restore	Tristan Croll	Tristan Croll	"{{{
The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-11-13)
Description
Saving/restoring with Clipper and ISOLDE active no longer causes a traceback, and the atomic model is returned on restore (any Volume instances subordinate to the SymmetryManager are lost, and will need to be reloaded by the user). The SymmetryManager restore_snapshot() just returns a generic Model. Not sure if this is desired behaviour, but in one instance I forgot to make SymmetryManager.restore_snapshot() actually *return* the Model, but to my surprise the AtomicStructure was still returned anyway - just placed at the top of the model tree. To be safe, I'm still returning the model so the restored tree looks like:

(Placeholder) Data manager (model name)
  |
  -- atomic model

Will get dev builds out with this basic behaviour, then work on doing it right.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-11-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3io0 format mmCIF fromDatabase pdb 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 ""intensity_meas, intensity_sigma"".  
notes | Resolution: 3.003  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0  
---  
Chain | Description  
1.3/A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> save test.cxs

Session saving is not yet implemented for ISOLDE. Custom restraints will not
be saved.  

Session saving for ChimeraX-Clipper objects is not yet fully implemented. Your
atomic model will be saved, but the symmetry and volume management framework
will not.  

> open test.cxs

Summary of feedback from opening test.cxs  
---  
notes | Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) MDFF potential  
Deleting (LIVE) 2mFo-DFc_sharp_29  
Deleting (LIVE) mFo-DFc  
Deleting Crystallographic maps (3io0-sf.cif)  
  
opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 418.87.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

}}}
"	defect	closed	normal		Third Party		fixed		chimera-programmers				all	ChimeraX