ISOLDE error

[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
Trying to restrain a selected hydrogen atom to pivot position in ISOLDE.  Apparently it cannot restrain hydrogen, probably requires a heavy atom.

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  
  

> isolde start

> set selectionWidth 4

Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> set bgColor white

> 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  
  

> hide HC

> isolde restrain ligands #1

QWidget::repaint: Recursive repaint detected  

> select #1

22945 atoms, 23062 bonds, 14 models selected  

> clipper spotlight

Setting spotlight mode for model 1.3 to True  

> view /B:383

> cofr centerOfView

> volume gaussian #1 sDev 0.75

> set bgColor black

> clipper associate #2 toModel #1

> select clear

> select clear

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.  
  

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  
reverting to start  
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.

[Tristan Croll]

Duplicate of #2515.

[pett]

actually assign some fields