mmCIF not handling 'oversampling' 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: 1.0 (2020-06-04 23:15:07 UTC)
Description
It looks like the mmCIF open command is no longer respecting the `overSampling` keyword that goes with `structureFactors true`. Should be a `FloatArg`.

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  

> open 6m5i structureFactors true

Summary of feedback from opening 6m5i fetched from pdb  
---  
notes | Fetching compressed mmCIF 6m5i from
http://files.rcsb.org/download/6m5i.cif  
Fetching compressed 6m5i structure factors from
http://files.rcsb.org/download/6m5i-sf.cif  
Resolution: 2.4959352905684393  
  
6m5i title:  
Crystal structure of 2019-nCoV nsp7-nsp8c complex [more info...]  
  
Chain information for 6m5i  
---  
Chain | Description  
1.2/A | SARS-CoV-2 nsp7  
1.2/B | SARS-CoV-2 nsp8  
  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 6m5i #1.2  
---  
notes | Termini for 6m5i (#1.2) chain B determined from SEQRES records  
Termini for 6m5i (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A SER 1  
Chain-initial residues that are not actual N termini: /B GLU 82  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /B ALA 196, /A THR 81  
235 hydrogen bonds  
Adding 'H' to /B GLU 82  
/B ALA 196 is not terminus, removing H atom from 'C'  
/A THR 81 is not terminus, removing H atom from 'C'  
1627 hydrogens added  
  

> hide HC

> isolde start

> set selectionWidth 4

Done loading forcefield  

> close #1.1.1.5-6

> select #1

3174 atoms, 3157 bonds, 26 models selected  

> select clear

> select clear

> view /A:73

> view /A:24

Updating bulk solvent parameters...  

> close #1

Deleting atomic symmetry model...  
Deleting (LIVE) MDFF potential  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_1  
Deleting Crystallographic maps (6m5i-sf.cif)  

> open 7bq7 structureFactors true

Summary of feedback from opening 7bq7 fetched from pdb  
---  
notes | Fetching compressed mmCIF 7bq7 from
http://files.rcsb.org/download/7bq7.cif  
Fetching compressed 7bq7 structure factors from
http://files.rcsb.org/download/7bq7-sf.cif  
Resolution: 2.3699641016055937  
  
7bq7 title:  
Crystal structure of 2019-nCoV nsp16-nsp10 complex [more info...]  
  
Chain information for 7bq7  
---  
Chain | Description  
1.2/A | SARS-CoV-2 nsp16  
1.2/B | SARS-CoV-2 nsp10  
  
Non-standard residues in 7bq7 #1.2  
---  
SAM — S-adenosylmethionine  
ZN — zinc ion  
  

> close #1.1.1.5-6

> select clear

> addh

Summary of feedback from adding hydrogens to 7bq7 #1.2  
---  
notes | Termini for 7bq7 (#1.2) chain A determined from SEQRES records  
Termini for 7bq7 (#1.2) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /A SER 1  
Chain-initial residues that are not actual N termini: /B ALA 18  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ASN 297, /B CYS 130  
627 hydrogen bonds  
Adding 'H' to /B ALA 18  
/A ASN 297 is not terminus, removing H atom from 'C'  
/B CYS 130 is not terminus, removing H atom from 'C'  
3348 hydrogens added  
  

> hide HC

> delete sel

> select clear

> 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")  

> save 7b7q_before.jpg supersample 3

> select clear

> select #1

6637 atoms, 6608 bonds, 3 pseudobonds, 27 models selected  
The following residues did not match any template: (SAM297)  

> select clear

> select :SAM

50 atoms, 52 bonds, 1 model selected  

> view sel

> view /B:88

> select #1

6637 atoms, 6608 bonds, 3 pseudobonds, 33 models selected  

> select clear

Updating bulk solvent parameters...  

> select up

69 atoms, 65 bonds, 1 model selected  

> select up

343 atoms, 348 bonds, 1 model selected  

> select clear

Updating bulk solvent parameters...  

> color bfactor

6637 atoms, 512 residues, atom bfactor range 32.5 to 205  

> color byattribute occupancy

6637 atoms, 512 residues, atom occupancy range 0 to 1  

> select clear

> color bychain

> color byhetero

> select clear

> select up

50 atoms, 47 bonds, 1 model selected  

> select up

232 atoms, 234 bonds, 1 model selected  

> select clear

Updating bulk solvent parameters...  

> isolde add water

> color sel bychain

> color sel byhetero

> isolde sim start sel

Updating bulk solvent parameters...  

> select up

3 atoms, 2 bonds, 1 model selected  

> delete sel

> color bfactor

6637 atoms, 512 residues, atom bfactor range 32.5 to 205  

> color bychain

> color byhetero

> select up

22 atoms, 21 bonds, 1 model selected  

> select up

231 atoms, 234 bonds, 1 model selected  

> select clear

Updating bulk solvent parameters...  

> select clear

> color bfactor

6637 atoms, 512 residues, atom bfactor range 32.5 to 205  

> color bychain

> color byhetero

> open 7b7q structureFactors true

Fetching url http://files.rcsb.org/download/7b7q.cif failed: HTTP Error 404:
Not Found  

> open 7bq7 structureFactors true

Summary of feedback from opening 7bq7 fetched from pdb  
---  
notes | Resolution: 2.3699641016055937  
  
7bq7 title:  
Crystal structure of 2019-nCoV nsp16-nsp10 complex [more info...]  
  
Chain information for 7bq7  
---  
Chain | Description  
2.2/A | SARS-CoV-2 nsp16  
2.2/B | SARS-CoV-2 nsp10  
  
Non-standard residues in 7bq7 #2.2  
---  
SAM — S-adenosylmethionine  
ZN — zinc ion  
  

> close #1.3#1-2#1.1-2#1.1.1#1.1.1.1-4,7

Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) MDFF potential  
Deleting (LIVE) 2mFo-DFc_smooth_7  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_7  
Deleting Crystallographic maps (7bq7-sf.cif)  
Deleting Crystallographic maps (7bq7-sf.cif)  

> open 7bq7 structureFactors true supersamp 2

Expected a keyword  

> open 7bq7 structureFactors true oversampling 2

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 382, in collated_open  
return func(*func_args, **func_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 72, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 332, in fetch_mmcif  
filename, format='mmcif', name=pdb_id, **kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/manager.py", line 164, in open_data  
_add_models=False, **kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 383, in collated_open  
return func(*func_args, **func_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 38, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
TypeError: open_mmcif() got an unexpected keyword argument 'oversampling'  
  
TypeError: open_mmcif() got an unexpected keyword argument 'oversampling'  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 38, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
  
See log for complete Python traceback.  
  

> usage clipper open

clipper open path [structureModel a structure specifier] [overSampling a
number]  
— Open a structure factor .mtz or .cif file and generate maps for the given
model  
path: name of a file to open/read  




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        8.8G         43G        336M         10G         53G
	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

[Eric Pettersen]

When I ported to the new 'open', missed the fact that the keyword is over_sampling rather than oversampling.