document pseudobond group create_type arg

[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: 0.93 (2020-04-03)
Description
Trying to get the metal coordination pseudobond group via the Python console fails:

{{{
m = session.models.list()[0]

m.pseudobond_group('metal coordination bonds')
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-11-987d3ef84bea> in <module>
----> 1 m.pseudobond_group('metal coordination bonds')

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molobject.py in pseudobond_group(self, name, create_type)
   1622                        args = (ctypes.c_void_p, ctypes.c_char_p, ctypes.c_int),
   1623                        ret = ctypes.py_object)
-> 1624         return f(self._c_pointer, name.encode('utf-8'), create_arg)
   1625 
   1626     def _delete_pseudobond_group(self, pbg):

TypeError: Group type mismatch
}}}

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed
'ChimeraX_ISOLDE-1.0b5.dev0-cp37-cp37m-linux_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/home/tic20/.cache/ChimeraX/0.93/installers/ChimeraX_ISOLDE-1.0b5.dev0-cp37-cp37m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.93 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-
ISOLDE==1.0b5.dev0) (0.93)  
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper==0.12.* in
/home/tic20/.local/share/ChimeraX/0.93/site-packages (from ChimeraX-
ISOLDE==1.0b5.dev0) (0.12.1)  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-
ISOLDE==1.0b5.dev0) (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==1.0b5.dev0) (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==1.0b5.dev0) (1.0)  
Installing collected packages: ChimeraX-ISOLDE  
Attempting uninstall: ChimeraX-ISOLDE  
Found existing installation: ChimeraX-ISOLDE 1.0b5.dev0  
Uninstalling ChimeraX-ISOLDE-1.0b5.dev0:  
Successfully uninstalled ChimeraX-ISOLDE-1.0b5.dev0  
Successfully installed ChimeraX-ISOLDE-1.0b5.dev0  
Lock 139908409982224 acquired on
/home/tic20/.cache/ChimeraX/0.93/toolshed/bundle_info.cache.lock  
Lock 139908409982224 released on
/home/tic20/.cache/ChimeraX/0.93/toolshed/bundle_info.cache.lock  
  

> open 1pmx format mmCIF fromDatabase pdb

Summary of feedback from opening 1pmx fetched from pdb  
---  
note |  
  
  
| Summary of feedback from opening /home/tic20/Downloads/ChimeraX/PDB/1pmx.cif  
  
---  
  
  
  
  
warnings | Atom H1 is not in the residue template for GLY #1 in chain A  
Atom H1 is not in the residue template for ARG #101 in chain B  
  
  
  
  
  
1pmx title:  
Insulin-like growth factor-I bound to A phage-derived peptide [more info...]  
  
Chain information for 1pmx  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | Insulin-like growth
factor IB  
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B
1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B | igf-1 antagonist
F1-1  
  
  

> 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")  

> color sel bychain

> color sel byhetero

> select #1.1/A:102@C

1 atom, 1 model selected  

> select up

20 atoms, 20 bonds, 1 model selected  

> select up

303 atoms, 308 bonds, 1 model selected  

> select up

2092 atoms, 2120 bonds, 1 model selected  

> select down

303 atoms, 308 bonds, 1 model selected  
Drag select of 1046 atoms, 1060 bonds  

> delete sel

> color sel bychain

> color sel byhetero

> close #1

> open 6os4 format mmCIF fromDatabase pdb

6os4 title:  
Calmodulin in complex with farnesyl cysteine methyl ester [more info...]  
  
Chain information for 6os4 #1  
---  
Chain | Description  
A | Calmodulin-1  
  
Non-standard residues in 6os4 #1  
---  
5U0 — s-farnesyl-l-cysteine methyl ester  
CA — calcium ion  
  
6os4 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| software_defined_assembly  
  
  




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
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

[Tristan Croll]

OK, I worked out from grepping through the ChimeraX codebase that I have to use create_type=None, but that's not documented in the pseudobond_group method.

[Eric Pettersen]

Okay, that argument is documented now.