id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2515	ISOLDE error when attempting to restrain hydrogens	goddard@…		"{{{
The following bug report has been submitted:
Platform:        Darwin-19.0.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-10-10)
Description
Restraining selected hydrogen  atom to pivot position generates this error.  I guess it requires a heavy atom.  Maybe it should restrain the attached heavy atom if a hydrogen is selected.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-10-10)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde tutorial

> isolde demo cryo_em modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description  
A B C | capsid protein VP1  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> clipper associate #2 toModel #1

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb  
---  
Chain | Description  
1.3/A 1.3/B 1.3/C | capsid protein VP1  
  

> addh

Summary of feedback from adding hydrogens to 6out.pdb #1.3  
---  
notes | Termini for 6out.pdb (#1.3) chain A determined from SEQRES records  
Termini for 6out.pdb (#1.3) chain B determined from SEQRES records  
Termini for 6out.pdb (#1.3) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /B THR 9  
Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29  
Chain-final residues that are actual C termini: /A SER 520  
Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519  
Missing OXT added to C-terminal residue /A SER 520  
1438 hydrogen bonds  
Adding 'H' to /A ASP 29  
Adding 'H' to /C ASP 29  
/B ALA 519 is not terminus, removing H atom from 'C'  
/C ALA 519 is not terminus, removing H atom from 'C'  
11439 hydrogens added  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  
Traceback (most recent call last):  
File ""/Users/goddard/Desktop/ChimeraX Oct 10
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/isolde.py"", line 1920, in
_restrain_selected_atom_to_pivot_xyz  
self.restrain_atom_to_xyz(atom, target, k)  
File ""/Users/goddard/Desktop/ChimeraX Oct 10
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/isolde.py"", line 1939, in restrain_atom_to_xyz  
pr.target = target  
AttributeError: 'NoneType' object has no attribute 'target'  
  
AttributeError: 'NoneType' object has no attribute 'target'  
  
File ""/Users/goddard/Desktop/ChimeraX Oct 10
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/isolde.py"", line 1939, in restrain_atom_to_xyz  
pr.target = target  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.0.68
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

}}}
"	defect	closed	major		Third Party		fixed						all	ChimeraX