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, 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> 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
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Elaine Meng -
Philipp Milkereit