[chimerax-users] Antw: [EXT] Re: selection modes

[Eric Pettersen]

You're welcome!  No, it didn't take too much time really.  Adding a control to make using the menu mode optional would have been more effort, and I may do that in the future if requested, but not for now...

--Eric

> On Jun 23, 2020, at 12:25 AM, Philipp Milkereit <philipp.milkereit at vkl.uni-regensburg.de> wrote:
> 
> Dear Eric,
>  
> thanks a lot! i hope it did not take too much of your time to integrate this workflow.
>  
> Philipp
>  
> Von: Eric Pettersen <pett at cgl.ucsf.edu> 
> Gesendet: Dienstag, 23. Juni 2020 01:18
> An: Philipp.Milkereit at vkl.uni-regensburg.de
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Betreff: Re: [chimerax-users] Antw: [EXT] Re: selection modes
>  
> Hi Philipp,
>                As of tomorrow's daily build, Basic Actions will honor the current Select menu mode.
>  
> --Eric
>  
>                Eric Pettersen
>                UCSF Computer Graphics Lab
>  
> 
> 
>> On Jun 18, 2020, at 9:29 AM, Elaine Meng <meng at cgl.ucsf.EDU <mailto:meng at cgl.ucsf.EDU>> wrote:
>>  
>> 
>> 
>>> From: "Philipp Milkereit" <Philipp.Milkereit at vkl.uni-regensburg.de <mailto:Philipp.Milkereit at vkl.uni-regensburg.de>>
>>> Subject: Antw: Re: [chimerax-users] Antw: [EXT] Re: selection modes
>>> Date: June 18, 2020 at 9:06:02 AM PDT
>>> To: <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
>>>  
>>> Hi Elaine
>>> just a follow-up question on the Select  Menu_Mode:Add, do you think it could make sense to apply this mode also to user-defined names listed in the Basic Actions window? That seems at the moment neither in ChimeraX 0.93 nor in 1.0 the case, but could be an easy way to add  fast a bunch of named selections to the current selection. Also for the subtract/intersect modes that might be an interesting option? 
>>>  
>>> best wishes,
>>>  
>>> Philipp
>>> >>> Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> 18.06.2020 17:33 >>>
>>> Hi Philipp,
>>> I don't think there is an ISOLDE for 1.0 yet.  If I look at the toolshed it says ISOLDE 1.05b "works with 0.93"
>>>  
>>> <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde>>
>>>  
>>> Best,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>>  
>>> > On Jun 18, 2020, at 1:18 AM, Philipp Milkereit <Philipp.Milkereit at vkl.uni-regensburg.de <mailto:Philipp.Milkereit at vkl.uni-regensburg.de>> wrote:
>>> > 
>>> > Dear Elaine,
>>> > 
>>> > thanks for your help!
>>> > Your example does not work for me on ChimeraX 0.93 (2020-04-03) both on a Windows and a Linux sytem.  But after installing the new production version 1.0 the selection mode works indeed there on user defined selectors as expected, which is great!
>>> > Apparently there should be also now versions of the Isolde plugin (1.0b5 ?) which are compatible with ChimeraX 1.0, so no reason anymore to stay with 0.93.. 
>>> > 
>>> > Best,
>>> > 
>>> > Philipp  
>>> > >>> Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> 18.06.2020 01:15 >>>
>>> > Hi Philipp,
>>> > This works fine for me using the menu.  For example, start ChimeraX, then:
>>> > 
>>> > open 2gbp
>>> > menu: Select... Structure... Secondary Structure... Strand
>>> > menu: Select... Define Selector... (I gave it the name "mystrands")
>>> > menu: Select... Clear
>>> > menu: Select... Structure... Ligand
>>> > menu: Select... Menu Mode... Add
>>> > menu: Select... User-Defined Selectors... mystrands
>>> > 
>>> > Now both the ligand and strands are selected.  Also works if I use commands for any of those steps.  When you use the menu, the corresponding commands are echoed in the Log, and it actually works by running the commands, so it doesn't make sense that commands would work and the menu wouldn't.
>>> > 
>>> > Tested in version 1.0.
>>> > 
>>> > I hope this helps,
>>> > Elaine
>>> > -----
>>> > Elaine C. Meng, Ph.D.                      
>>> > UCSF Chimera(X) team
>>> > Department of Pharmaceutical Chemistry
>>> > University of California, San Francisco
>>> > 
>>> > 
>>> > > On Jun 17, 2020, at 1:11 PM, Philipp Milkereit <philipp.milkereit at vkl.uni-regensburg.de <mailto:philipp.milkereit at vkl.uni-regensburg.de>> wrote:
>>> > >
>>> > > Dear all,
>>> > > 
>>> > > is there a way to add user-defined selectors or named selections (command: name) to the current selection by choosing them from the Menu:Select or in the Basic Actions window? Changing to Menu_Mode:Add in Menu:Select seems not to have any effect on that. I think in Chimera1 named selections still could be added to the current selection using the „append“ selection mode. At the moment adding named selections to the current selection works for me in ChimeraX just with the command line „select add“ command.
>>> > > 
>>> > > Many thanks for your help,
>>> > > 
>>> > > Philipp Milkereit
>> 
>>  
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