open/save severely hampered

[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 (2020-05-05)
Description
"open {pdb id}" now fails, unless I explicitly add the "fromdatabase pdb" argument.

Log:
UCSF ChimeraX version: 1.0rc202005052344 (2020-05-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> open 3io0 structureFa t

'3io0' has no suffix  

> open 3io0 fromDatabase pdb

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #1  
---  
Chain | Description  
A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0  
---  
Chain | Description  
1.2/A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> close #1

Deleting atomic symmetry model...  

> open 3io0 fromDatabase pdb structureFactors true

Summary of feedback from opening 3io0 fetched from pdb  
---  
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 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0  
---  
Chain | Description  
1.2/A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_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]

Also, the "save" command has lost most of its formats (including PDB/mmCIF). Saving via the File menu still works. Could have sworn I submitted a separate bug report from within ChimeraX, but can't see it here or in my email.

[Eric Pettersen]

My release candidate download suffers none of the problems you are describing. However, it's for the Mac and the version number is different from yours. Mine is 1.0rc202005052350 whereas yours is 1.0rc202005052344.

Greg, how is this possible? Shouldn't the version numbers be the same?

[Tristan Croll]

I haven't updated the Clipper and ISOLDE bundles to use your new 
open/save framework (was about to start). Could that be disrupting 
things?

On 2020-05-06 16:34, ChimeraX wrote:

[Eric Pettersen]

No, not as far as I know. The only way you should be able to get that message is if you literally had a file named "3io0" in your current directory, and that still wouldn't explain the "save" problems.

I'd still like to know how your version could have a different version number. Greg?

[Eric Pettersen]

I guess get tomorrow's build. If the problem doesn't disappear, I'll have you try various Python-y things to try to find out what the devil is going on! :-)

[Greg Couch]

The version numbers are based on the last git check in. Perhaps the difference is that Tristan had the version distributed on the download page, and Eric's version was from a local build that was from a more recent checkout?

[Eric Pettersen]

No, mine was downloaded from the web page. I hadn't even build from the 1.0 source yet at that point.

[Greg Couch]

There might have been an earlier version on the website, we only keep one per day, and Tristan happened to get it. Don't anticipate it being much of a problem going forward.

[Tristan Croll]

Updated to today's build, and the problems persist. Version now reports as 1.0rc202005070439 (2020-05-07).

open 3io0 structurefa t
# Error: '3io0' has no suffix

open 3io0 fromDatabase pdb
# works

open 3io0 fromDatabase pdb structureFactors true
# works

save test.pdb #1
# Error: Expected a keyword

save test.pdb
# works

save test.pdb models #1
# works

... So it seems I was mistaken (sorry!). It's not that the format isn't registered, it's just that the behaviour has changed (the models argument now needs to be explicitly specified as a keyword where before it didn't). Same for mmCIF format.

[Eric Pettersen]

Move chimerax.open_command.cmd.py aside and replace it with this:

cmd.py​

Should put some info in the log as you try “open 3io0”.  Let me know what it logs.

—Eric

[Eric Pettersen]

Added by email2trac

[Eric Pettersen]

Since this seems to be a Tristan-only problem, which reduces the urgency somewhat, I am taking chimera-programmers off the cc list.

[Eric Pettersen]

Okay, put T.G. back on, since he probably cares about the 'save models' keyword thing, which I will be working on.

[Eric Pettersen]

Should have tested the damn script before I sent it.  It had a minor bug.  Here’s a corrected version:

cmd-1.py​

[Eric Pettersen]

Added by email2trac

[Eric Pettersen]

Okay, 'save' command now allows 'models' keyword to alternatively be specified as the second positional argument

[Tristan Croll]

Here's what I get in the log:

UCSF ChimeraX version: 1.0rc202005070439 (2020-05-07)
© 2016-2020 Regents of the University of California. All rights 
reserved.
How to cite UCSF ChimeraX
no database and exists[1]
open 3io0no database and exists[1]
'3io0' has no suffix


On 2020-05-07 17:12, ChimeraX wrote:

[Tristan Croll]

Ah! So that explains *that* problem: the directory I happened to be 
running ChimeraX from has a directory called "3io0" in it. Change to a 
different working directory, and it's fine again. Perhaps change the 
call from `os.path.exists(file_name)` to `os.path.isfile(file_name)`?

On 2020-05-07 18:27, ChimeraX wrote:

[Eric Pettersen]

It's more complicated than that, since there are formats that open directories (e.g. DICOM). I'll see what I can do.

[Tristan Croll]

That *does* make things more complicated, I agree. But I imagine that 
people having directories named after PDB IDs is a scenario that could 
crop up at a non-trivial rate.

On 2020-05-07 18:42, ChimeraX wrote:

[Eric Pettersen]

Okay, I've committed a fix that works in my testing.