Re: [chimerax-users] Antw: [EXT] Re: selection modes
From: "Philipp Milkereit" <Philipp.Milkereit@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@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@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@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@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@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
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@cgl.ucsf.EDU> wrote:
From: "Philipp Milkereit" <Philipp.Milkereit@vkl.uni-regensburg.de <mailto:Philipp.Milkereit@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@cgl.ucsf.edu <mailto:meng@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@cgl.ucsf.edu <mailto:meng@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@vkl.uni-regensburg.de <mailto:Philipp.Milkereit@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@cgl.ucsf.edu <mailto:meng@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@vkl.uni-regensburg.de <mailto:philipp.milkereit@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@cgl.ucsf.edu> Gesendet: Dienstag, 23. Juni 2020 01:18 An: Philipp.Milkereit@vkl.uni-regensburg.de Cc: ChimeraX Users Help <chimerax-users@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@cgl.ucsf.EDU <mailto:meng@cgl.ucsf.EDU> > wrote: From: "Philipp Milkereit" <Philipp.Milkereit@vkl.uni-regensburg.de <mailto:Philipp.Milkereit@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@cgl.ucsf.edu <mailto:meng@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@cgl.ucsf.edu <mailto:meng@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> 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@vkl.uni-regensburg.de <mailto:Philipp.Milkereit@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@cgl.ucsf.edu <mailto:meng@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@vkl.uni-regensburg.de <mailto:philipp.milkereit@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@cgl.ucsf.edu> Gesendet: Dienstag, 23. Juni 2020 01:18 An: Philipp.Milkereit@vkl.uni-regensburg.de Cc: ChimeraX Users Help <chimerax-users@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@cgl.ucsf.EDU <mailto:meng@cgl.ucsf.EDU>> wrote:
From: "Philipp Milkereit" <Philipp.Milkereit@vkl.uni-regensburg.de <mailto:Philipp.Milkereit@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@cgl.ucsf.edu <mailto:meng@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@cgl.ucsf.edu <mailto:meng@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@vkl.uni-regensburg.de <mailto:Philipp.Milkereit@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@cgl.ucsf.edu <mailto:meng@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@vkl.uni-regensburg.de <mailto:philipp.milkereit@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
participants (3)
-
Elaine Meng -
Eric Pettersen -
Philipp Milkereit