Chimera→ChimeraX session converter

[Zach Pearson]

This is a meta-ticket to track the effort to support Chimera sessions in ChimeraX. I’ve been told that the status of this is tracked at the top of a Python file in the Chimera repo, but I’ll be converting the issues listed there to tickets if they don't already exist. Then, those tickets will be categorized as blocking this one.

[Zach Pearson]

List of the todos at the top of the relevant file.

#TODO: custom sequence headers and have non-wrapping alignments float (see "How to view consurf results in chimerax" in ChimeraX/seq mbox
#TODO: nucleotides is a _lot_ of work
#TODO: then: per-model clipping (as best we can)
#TODO: then: 2D arrows
#TODO: then: volumes
#TODO: update ChimeraX message when opening .py files to say volumes okay
#TODO: then: sequences: intrinsic; finish headers (settings); letter coloring(?)
#TODO: planes/axes/centroids

[Eric Pettersen]

Done: custom headers / having non-wrapping alignments float

[Eric Pettersen]

Done: per-model clipping

[Zach Pearson]

Just noting some other missing features we have listed from the ChimeraX downloads page. Are any of these things to do with sessions? Are any of them out of date?

ChimeraX has several completely new features compared to Chimera (see advantages), but not yet all of its commonly used capabilities. Some features are implemented as commands only, not (yet) as graphical interfaces. Missing features include charge assignment and parametrization of nonstandard residues (except in the ISOLDE plugin), dock prep, saving and restoring scenes, animation GUI, 2D label GUI, render by attribute GUI, “worms” to show residue attributes, trajectory analysis other than simple playback, calculating a multiple sequence alignment from a multiple structure superposition, and many others. Chimera capabilities grew significantly over several years, and likewise, ChimeraX will contain more of these important features as development proceeds.

Do we have missing features documented anywhere else?

[Eric Pettersen]

Well, a couple of those affect session migration tangentially in that you can't export session state for a capability that doesn't exist in ChimeraX. Among those listed, Chimera supports scenes and ChimeraX does not and therefore scene state cannot be exported. ChimeraX does not support "worms" depictions and therefore any worms depiction will be lost by the exporter (it will show a normal ribbon instead). The others don't really affect the exporter since I was never intending to export *tool* state anyway, just data state.

We don't keep a list of missing features anywhere else. The missing feature list is up to date, though it is not exhaustive. We only listed the features we felt were most important to users, particularly users contemplating switching.

[Eric Pettersen]

Another "TODO" if possible: preserve ViewDock info

[Eric Pettersen]

2D arrows now exported.

[Tom Goddard]

I added volume session conversion from Chimera to ChimeraX. All the changes are in Chimera in the chimerax.py file. Tested exporting surfaces, meshes, image style, orthoplanes and box rendering.

There are many other volume-related things that are not currently converted: coloring by radius, coloring by volume value, surface zone, color zone. I do not plan on adding those to the conversion code unless a user needs it. I suspect very few people are going to convert sessions. A research project is likely to be done all in Chimera without switching half-way to ChimeraX, so I don't expect session conversion to get much use.

[Eric Pettersen]

I expect session conversion to get most use when a researcher comes back to a project after a lapse of a few months or years, or when tweaking figures from a paper for a new paper or a poster. I similarly don't expect many switches "half way" through a continuously worked-on project.

[Tom Goddard]

Added Elaine to ticket so she can document the converter capabilities.

[Elaine Meng]

Thanks, I've updated and committed the export docs.

[Zach Pearson]

It sounds like we've done all of the upfront work on this and can open new tickets for as-needed work.