Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers
Oli
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers
Oli
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Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!).
It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.
Cheers
Oli
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
Tom
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers
Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc?
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