[chimerax-users] Next/previous buttons?

vincent Chaptal vincent.chaptal at ibcp.fr
Thu Feb 3 00:20:59 PST 2022 

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> 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> 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> 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> 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> 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> 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> 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
>>>>>>>>
>>>>>>>> Tom
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users 
>>>>>>>>> <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


MMSB -UMR5086

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