[Chimera-users] Three suggestions

Antoine Maillard antoine.maillard at ibs.fr
Wed Apr 10 09:54:51 PDT 2013


Dear Eric,

Thank you for your replies and your quick implementation of an automated 
refresh for named selections!

Concerning suggestion #1:   changing Chain ID of a portion of a chain 
was meant to assist matchmaker in targeting the right domain and not let 
it take adventice (meaningless) pieces into account. I realize now that 
this could be quiet a challenge for Chimera to interpret in all the 
procedures already available... and will stick to the 
cut-into-domains-of-interest approach.

About suggestion #2: the ~namesel command that you proposed would allow 
to edit the listing, which is sometimes useful, i.e.  when you happen to 
get more and more named selections, sometimes similar in different 
models, and realize the names given were not specific enough. That would 
be nice!

Suggestion #3: if this is a problem then leave it where it stands!
(In case it is not: would it sound more reasonable to offer the 
window-size memorization as a tickable option? Could the window-location 
memorization and the tiling be combined when the "same" window is to be 
opened more than once?)

All in all, suggestion #2 might make it: that's a big thank you already!
Cheers,

Antoine

Antoine Maillard wrote:
>> Dear Chimera developpers,
>>
>> Thank you so much for your work and your dedication!
>> Having used Chimera quiet intensively recently, I have listed a few suggestions for your consideration.
>>
>> Suggestion #1:
>> Tools > Structure Editing > Change Chain IDs: lacks a "restrict to current selection" button (would allow to name various domains of a single protein)
> Are these domains disconnected from one another?  Because I don't think there are many programs (including Chimera) that will like connected polypeptide chains that change chain IDs in the middle.  If we're talking about disconnected domains then I can see the usefulness.  Otherwise I would think that a named selection or and alias would be more appropriate -- and more descriptive.
>
>> Suggestion #2:
>> Named selections: - I did not find out how to edit them (even "suppress" would add flexibility and reliability).
>>                                  - The list is not refreshed as session is closed (Windows). Thus opening and closing sessions one after the other results in merging the "Named selections" of all sessions successively opened...
> In the current daily build if a named selection becomes empty (which will happen during session close for example) it will delete itself.  Does this meet the need you're describing?  Otherwise I could implement ~namesel for deleting them even when they're not empty...
>
>> Suggestion #3:
>> The 'window-size memory' feature that was devised by Eric for the File>Open window would be of interest to most windows: model panel / matchmaker / match / etc... Could you make it a general feature of the various windows in the GUI?
> Well, due to the way the windowing library we use (Tk) works, it is quite a headache to impose an overall size on a window a priori.  The File->Open thing works by imposing a size on the browser widget inside the window and the window adjusts to compensate.  I wouldn't want to try to do this on a generic window basis.  Nonetheless, for certain dialogs where it would be high value (i.e. that get a lot of use and that are resized initially a lot) I could see implementing it.  The Model Panel comes to mind as you suggested.  I'd listen to other suggestions...
>
>> (It would also be a plus if the preferred location of any of these windows could be memorized as well.)
> This has been suggested and I have thought about it.  The are several problems.  One is that it doesn't work well with tiling.  Say you bring up some dialogs that get tiled.  Then you bring up a dialog whose placement is remembered, and it is right on top of the tiled dialogs.  Or say you make the main Chimera window larger today that you did yesterday -- there's an excellent chance that the memorized positions will be on top of the larger window.  Or you put the Chimera window on the right side of your display instead of the left side.  Or you put it on a second monitor.  I think you get the idea.
>
> --Eric
>
>                          Eric Pettersen
>                          UCSF Computer Graphics Lab
>                          http://www.cgl.ucsf.edu
>
>> I trust your expert appreciation whether these suggestions are to be implemented sooner or later... or never :-(
>> Thank you for your consideration and for your help!
>>
>> Antoine
>>
>>
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> Message: 4
> Date: Tue, 9 Apr 2013 14:49:40 -0700
> From: Eric Pettersen<pett at cgl.ucsf.edu>
> To: Eric Pettersen<pett at cgl.ucsf.edu>
> Cc:chimera-users at cgl.ucsf.edu, Antoine Maillard
> 	<antoine.maillard at ibs.fr>
> Subject: Re: [Chimera-users] Three suggestions
> Message-ID:<0FC38255-9642-419A-AC37-2055DA14366E at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> On Apr 9, 2013, at 2:45 PM, Eric Pettersen wrote:
>
>>> Suggestion #2:
>>> Named selections: - I did not find out how to edit them (even "suppress" would add flexibility and reliability).
>>>                                  - The list is not refreshed as session is closed (Windows). Thus opening and closing sessions one after the other results in merging the "Named selections" of all sessions successively opened...
>> In the current daily build if a named selection becomes empty (which will happen during session close for example) it will delete itself.  Does this meet the need you're describing?  Otherwise I could implement ~namesel for deleting them even when they're not empty...
> Forgot to mention that if you need to change the contents, you can just define them a second time.
>
> --Eric
>
>
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