Opening structure-factor cif

[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: 1.0rc202005270557 (2020-05-27 05:57:28 UTC)
Description
I might be mistaken, but I vaguely recall Eric saying that the new Open/Save framework should be able to distinguish between different file types with the same extensions based on arguments, but that doesn't seem to be the case here. If I register Clipper as a Provider to open cif format:

      <Provider name="sfCIF" category="Structure factors" suffixes=".cif"
          encoding="utf-8"/>

... then it appears to entirely override the atomic mmCIF format. Will disable it (it's still available as the "clipper open" command as always).

Log:
UCSF ChimeraX version: 1.0rc202005270557 (2020-05-27)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3io0.pdb

3io0.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for 3io0.pdb #1  
---  
Chain | Description  
A | predicted microcompartment protein  
  

> open 3io0-sf.cif structureModel #1

Summary of feedback from opening 3io0-sf.cif  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "intensity_meas, intensity_sigma".  
notes | Resolution: 3.003  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
3io0.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for 3io0.pdb  
---  
Chain | Description  
1.2/A | predicted microcompartment protein  
  
Opened crystallographic dataset from 3io0-sf.cif  
Found experimental reflection data:  
intensity_meas, intensity_sigma  
French and Wilson Amplitudes  
Rwork: 0.2014; Rfree: 0.2106  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_sharp_29  
Any unwanted maps may be safely closed via the Model panel.  

> open 3io0-sf.cif

Must specify a structure model to associate with crystallographic data  

> open 3io0.cif

Must specify a structure model to associate with crystallographic data  

> save test.mtz

Writing data to: '/*/*/[FOBS, SIGFOBS]'  

> save test.mtz #1

Writing data to: '/*/*/[FOBS, SIGFOBS]'  




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        5.2G         46G        298M         10G         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

[Tristan Croll]

To be clear, to date opening structure factor cif format has never been possible via the "open" command - just wanted to test if it would work now.

[Eric Pettersen]

No, you've got that backwards, given a format/suffix the open command knows what corresponding arguments are legal -- not the other way around. You can't have suffixes that clash with another format's suffixes. Your options are to use a unique suffix like ".sfcif" or to omit suffixes entirely and use the 'format' keyword when opening ("open blah.cif format sfcif").

[Tristan Croll]

Ah - my bad!

On 2020-06-01 17:56, ChimeraX wrote:

[Eric Pettersen]

Or both options. For files ending in .sfcif you could omit the format keyword and for those ending in .cif you would have to provide it.

[Tristan Croll]

I'll go with just allowing the format keyword for now. Will think about 
adding the ".sfcif" extension, but since that's not a standard used 
anywhere else I'm not convinced it'll get used much. Not a huge issue - 
for the vast majority of people the only time the structure factor CIF 
format is used is in fetching from the wwPDB (where "open {pdb_id} 
structureFactors true" circumvents the need to explicitly open the file 
anyway). All current tools I know of use MTZ internally.

On 2020-06-01 18:03, ChimeraX wrote:

[Eric Pettersen]

Your plan sounds good.