Chain mix up using ISOLDE

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.0 (2020-05-09)
Description
Just had a *really* weird glitch (that I can't replicate). Opened 6yyt and its map (EMD 11007), associated with Clipper, added hydrogens, started ISOLDE and tried to simulate... at which point somehow chain P had been reassigned as chain Q. Since there was already another chain Q (identical in sequence to P) ISOLDE refused to start a simulation. After working out what was going on I closed the model, which caused a segmentation fault (unfortunately I didn't have core dumps enabled, so didn't catch it for analysis). Reopened everything, and this time it all works fine.

Log:
UCSF ChimeraX version: 1.0rc202005090702 (2020-05-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6yyt

6yyt title:  
Structure of replicating SARS-CoV-2 polymerase [more info...]  
  
Chain information for 6yyt #1  
---  
Chain | Description  
A | nsp12  
B D | nsp8  
C | nsp7  
P Q T U | RNA product  
  
Non-standard residues in 6yyt #1  
---  
ZN — zinc ion  
  

> open 11007 fromDatabase emdb

Opened emd_11007.map, grid size 240,240,240, pixel 0.834, shown at level 3.34,
step 1, values float32  

> select /P

298 atoms, 332 bonds, 1 model selected  

> select /Q

298 atoms, 332 bonds, 1 model selected  

> clipper associate #2 toModel #1

6yyt title:  
Structure of replicating SARS-CoV-2 polymerase [more info...]  
  
Chain information for 6yyt  
---  
Chain | Description  
1.2/A | nsp12  
1.2/B 1.2/D | nsp8  
1.2/C | nsp7  
1.2/P 1.2/Q 1.2/T 1.2/U | RNA product  
  
Non-standard residues in 6yyt #1.2  
---  
ZN — zinc ion  
  

> select /P

298 atoms, 332 bonds, 1 model selected  

> select /Q

298 atoms, 332 bonds, 1 model selected  

> select /P:5@OP2

1 atom, 1 model selected  

> preset custom "make bond"

> open /home/tic20/chimerax_presets/make_bond.py

executed make_bond.py  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select clear

> select /P

298 atoms, 332 bonds, 1 model selected  

> select /Q

298 atoms, 332 bonds, 1 model selected  

> addh

Summary of feedback from adding hydrogens to 6yyt #1.2  
---  
warnings | Not adding hydrogens to /B PHE 6 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /B SER 7 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B SER 8 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B SER 11 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B TYR 12 CB because it is missing heavy-atom bond
partners  
23 messages similar to the above omitted  
Unknown hybridization for atom (P) of residue type C; not adding hydrogens to
it  
notes | Termini for 6yyt (#1.2) chain A determined from SEQRES records  
Termini for 6yyt (#1.2) chain B determined from SEQRES records  
Termini for 6yyt (#1.2) chain C determined from SEQRES records  
Termini for 6yyt (#1.2) chain D determined from SEQRES records  
Termini for 6yyt (#1.2) chain P determined from SEQRES records  
3 messages similar to the above omitted  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A VAL 31, /A PHE 77, /A
ARG 118, /B PHE 6, /C SER 1, /D PHE 6, /P C 5, /Q C 5, /T U 7, /U C 5  
Chain-final residues that are actual C termini: /P G 18, /Q G 18, /T G 18, /U
G 18  
Chain-final residues that are not actual C termini: /A LYS 50, /A ALA 97, /A
THR 929, /B ALA 191, /C GLU 73, /D ALA 191  
1178 hydrogen bonds  
Adding 'H' to /A VAL 31  
Adding 'H' to /A PHE 77  
Adding 'H' to /A ARG 118  
Adding 'H' to /B PHE 6  
Adding 'H' to /C SER 1  
1 messages similar to the above omitted  
/A LYS 50 is not terminus, removing H atom from 'C'  
/A ALA 97 is not terminus, removing H atom from 'C'  
/A THR 929 is not terminus, removing H atom from 'C'  
/B ALA 191 is not terminus, removing H atom from 'C'  
/C GLU 73 is not terminus, removing H atom from 'C'  
1 messages similar to the above omitted  
10617 hydrogens added  
  

> hide HC

> select /P

451 atoms, 485 bonds, 1 model selected  

> select /Q

450 atoms, 484 bonds, 1 model selected  

> select /T

387 atoms, 416 bonds, 1 model selected  

> select /U

451 atoms, 485 bonds, 1 model selected  

> delete nucleic&@H

> delete nucleic&@HP1

> toolshed show Shell

/opt/UCSF/ChimeraX/lib/python3.7/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

21988 atoms, 22327 bonds, 72 pseudobonds, 10 models selected  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> select clear

> select #1

21988 atoms, 22327 bonds, 72 pseudobonds, 15 models selected  

> select clear




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        6.4G         46G        227M         10G         55G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia

[Eric Pettersen]

Well, chain IDs did become writable on Tuesday, though it's hard to do outside of Python (an esoteric setattr command will do it), and besides, it would probably also need to be new code doing it since trying to write the ID before would have been a error. So agreed: weird.

[Tristan Croll]

Well, I certainly haven't added any code to mess with chain IDs (although it's a useful new feature that undoubtedly will come in handy later). A slightly disturbing event...