Leave hydrogens intact if atom modification impossible
The following bug report has been submitted:
Platform: Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Playing around to test the behaviour of `build_structure.modify_atom()`: if I ask it to increase the number of bonds beyond what the chemistry can support, it correctly throws an error - but it also deletes any hydrogens that were attached to that atom. Of course I can put them back in a try...except - but this doesn't seem like ideal behaviour.
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Successfully installed 'ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl'
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing
/home/tic20/.cache/ChimeraX/1.0/installers/ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper~=0.13.0 in
/home/tic20/.local/share/ChimeraX/1.0/site-packages (from ChimeraX-
ISOLDE==1.0rc1) (0.13.0)
Requirement already satisfied, skipping upgrade: ChimeraX-
Core~=1.0rc202005052344 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages
(from ChimeraX-ISOLDE==1.0rc1) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1)
(1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Arrays~=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1)
(1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Graphics~=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-
Atomic>=1.0->ChimeraX-ISOLDE==1.0rc1) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Geometry~=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-
Atomic>=1.0->ChimeraX-ISOLDE==1.0rc1) (1.0)
Installing collected packages: ChimeraX-ISOLDE
Attempting uninstall: ChimeraX-ISOLDE
Found existing installation: ChimeraX-ISOLDE 1.0rc1
Uninstalling ChimeraX-ISOLDE-1.0rc1:
Successfully uninstalled ChimeraX-ISOLDE-1.0rc1
Successfully installed ChimeraX-ISOLDE-1.0rc1
Lock 140608444654928 acquired on
/home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock
Lock 140608444654928 released on
/home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock
WARNING: You are using pip version 20.1; however, version 20.2 is available.
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.
> ui tool 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")
> open /home/tic20/.local/share/ChimeraX/1.0/site-
> packages/chimerax/isolde/demo_data/3io0/before.pdb format pdb
before.pdb title:
Crystal structure of etub from clostridium kluyveri [more info...]
Chain information for before.pdb #1
---
Chain | Description
A | predicted microcompartment protein
> show
> select /A:159@CE1
1 atom, 1 model selected
> show
> select /A:116@CD1
1 atom, 1 model selected
OpenGL version: 3.3.0 NVIDIA 450.51.05
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 5.1G 48G 165M 8.8G 56G
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
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History
(3)
Component: |
Unassigned → Structure Editing
|
Platform: |
→ all
|
Project: |
→ ChimeraX
|
Summary: |
ChimeraX bug report submission → Leave hydrogens intact if atom modification impossible
|
Type: |
defect → enhancement
|
Owner: |
set to Eric Pettersen
|
Status: |
new → accepted
|
Resolution: |
→ fixed
|
Status: |
accepted → closed
|