[chimerax-users] Next/previous buttons?
Oliver Clarke
olibclarke at gmail.com
Mon Feb 7 06:20:48 PST 2022
Hi all,
Here is a quick screen recording:
https://www.dropbox.com/s/jlbhbjqy9mdrb74/screen_recording_next_prev.mov?dl=0 <https://www.dropbox.com/s/jlbhbjqy9mdrb74/screen_recording_next_prev.mov?dl=0>
This is a mock up, so there's not much interesting to see, but in this case I am comparing different maps from the output of a 3D classification run with an atomic model. The interface in chimera allows me to easily and quickly compare all the classes to both each other and to the atomic model, identify the good ones and then compare those, while deselecting the others, quickly flick between just two classes, and then to compare two classes with a fixed third class.
Currently I find it hard to do anything like this in ChimeraX, but it may be just that I haven't spent enough time with it.
In "real" examples I would be looking for subtle conformational differences (or perhaps the presence/absence of a ligand/ion/water at higher resolution) between the classes, which flicking quickly between maps can help discern, but there is not much to see on that front here - does this recording make it easier to understand the use case?
Cheers
Oli
> On Feb 7, 2022, at 8:42 AM, Guillaume Gaullier <guillaume.gaullier at icm.uu.se> wrote:
>
> Sorry, I sent my previous answer before I finished reading the discussion. My use case is mostly to compare many maps that are already aligned (or already close enough that I don’t need to align them anyway), and I need to be able to do things like:
>
> 1. scroll through all maps (vseries does this very well, with the slider or play button if I want to let it cycle through the series),
> 2. keep any number of maps with arbitrary indices displayed, while scrolling through all other maps,
> 3. display any number of maps with arbitrary indices while hiding all the others
>
> 1 is easy to do with vseries. 2 and 3 are doable with the model panel checkboxes, but are tedious and clicking-intensive beyond about 10 maps (and typical work easily gets you 50 maps to look at) since you need to uncheck map n and check map n+1 every time you want to show the next map. 3 is doable with a command, so I should study the model selection syntax more closely and stop complaining. But I can’t see how to do 2 with a command.
>
> So everything I need to do is doable with ChimeraX in its current form, but if some of these things required less clicks I would not shy away from looking at more than 50 maps.
>
> I hope this description helps understanding the use case. Curious to see the screen recording from Oli.
> Cheers,
>
> Guillaume
>
>
>> On 3 Feb 2022, at 23:56, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>
>> Hi Vincent,
>>
>> I'm glad to hear from all of you about this need. I get how mseries or the Chimera next/prev/skip buttons allows you flip through maps or class average images. Oliver wants some finer control than mseries allows and the Chimera user interface is cumbersome (rows of checkbuttons for every model) and I am missing the fine details of how the comparisons are done in practice that would allow an improved capability. For instance astronomers will quickly flip back and forth between two perfectly aligned images of the sky to see if anything changed (e.g. a supernova) -- the comparison requires fast aligned flipping repeated many times. I don't understand the precise kinds of comparisons you, Guillaume and Oliver are talking about, so it is hard to develop anything to help.
>>
>> Tom
>>
>>> On Feb 3, 2022, at 12:20 AM, vincent Chaptal <vincent.chaptal at ibcp.fr <mailto:vincent.chaptal at ibcp.fr>> wrote:
>>>
>>> Hi,
>>>
>>> we use the mseries a lot to compare maps and create movies.
>>> It is really great and allows for preliminary observations. Now that we are now moving in more detailed examinations, I can see where Oliver's query goes and is interesting. I also think it's not a niche but the future of cryoEM observations.
>>>
>>> More tools along these lines could only be an asset.
>>> Best
>>> Vincent
>>>
>>> Le 02/02/2022 à 21:58, Tom Goddard via ChimeraX-users a écrit :
>>>> Hi Guillaume,
>>>>
>>>> The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
>>>>
>>>> Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
>>>>
>>>> Tom
>>>>
>>>>> On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <guillaume.gaullier at icm.uu.se <mailto:guillaume.gaullier at icm.uu.se>> wrote:
>>>>>
>>>>> 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,
>>>>>
>>>>> Guillaume
>>>>>
>>>>>
>>>>>> On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>>>>>
>>>>>> 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
>>>>>>
>>>>>>> On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>> On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>>>>>>>
>>>>>>>> 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
>>>>>>>>
>>>>>>>> <PastedGraphic-1.png>
>>>>>>>>
>>>>>>>>> On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>>>>>>>>
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>>> On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>>>>>>>>>
>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>>> On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>>>>>>>>>>
>>>>>>>>>>> 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.
>>>>>>>>>>>
>>>>>>>>>>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html>
>>>>>>>>>>>
>>>>>>>>>>> Tom
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> 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?
>>>>>>>>>>>> <PastedGraphic-1.png>
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>>> --
>>> Vincent Chaptal, PhD
>>> Director of GdR APPICOM
>>> Drug Resistance and Membrane Proteins Lab
>>>
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>
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