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</o:shapelayout></xml><![endif]--></head><body lang=DE link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='mso-fareast-language:EN-US'>Dear Eric,<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>thanks a lot! i hope it did not take too much of your time to integrate this workflow.<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>Philipp<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b>Von:</b> Eric Pettersen <pett@cgl.ucsf.edu> <br><b>Gesendet:</b> Dienstag, 23. Juni 2020 01:18<br><b>An:</b> Philipp.Milkereit@vkl.uni-regensburg.de<br><b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br><b>Betreff:</b> Re: [chimerax-users] Antw: [EXT] Re: selection modes<o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Philipp,<o:p></o:p></p><div><p class=MsoNormal><span class=apple-tab-span> </span>As of tomorrow's daily build, Basic Actions will honor the current Select menu mode.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><div><p class=MsoNormal>--Eric<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span>Eric Pettersen<o:p></o:p></p></div><div><p class=MsoNormal><span class=apple-tab-span> </span>UCSF Computer Graphics Lab<o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On Jun 18, 2020, at 9:29 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.EDU">meng@cgl.ucsf.EDU</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal><b><span style='font-family:"Helvetica",sans-serif'>From: </span></b><span style='font-family:"Helvetica",sans-serif'>"Philipp Milkereit" <<a href="mailto:Philipp.Milkereit@vkl.uni-regensburg.de">Philipp.Milkereit@vkl.uni-regensburg.de</a>></span><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Helvetica",sans-serif'>Subject: Antw: Re: [chimerax-users] Antw: [EXT] Re: selection modes</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Helvetica",sans-serif'>Date: </span></b><span style='font-family:"Helvetica",sans-serif'>June 18, 2020 at 9:06:02 AM PDT</span><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='font-family:"Helvetica",sans-serif'>To: </span></b><span style='font-family:"Helvetica",sans-serif'><<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>></span><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><div id="GroupWiseSection_1592495672000_Philipp.Milkereit@vkl.uni-regensburg.de_DA56788005CB0000B1281300A700BE00_"><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>Hi Elaine<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>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? <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>best wishes,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>Philipp<o:p></o:p></span></p></div><div id="GroupWiseSection_1592494430000_meng@cgl.ucsf.edu"><p class=MsoNormal><span class=groupwisereplyheader><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>>>> Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> 18.06.2020 17:33 >>></span></span><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'><o:p></o:p></span></p><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>Hi Philipp,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>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"<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'><o:p> </o:p></span></p></div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'><<a href="https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde">https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde</a>><o:p></o:p></span></p><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>Best,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>Elaine<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>-----<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>Elaine C. Meng, Ph.D. <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>UCSF Chimera(X) team<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>Department of Pharmaceutical Chemistry<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>University of California, San Francisco<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> On Jun 18, 2020, at 1:18 AM, Philipp Milkereit <<a href="mailto:Philipp.Milkereit@vkl.uni-regensburg.de">Philipp.Milkereit@vkl.uni-regensburg.de</a>> wrote:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> Dear Elaine,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> thanks for your help!<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> 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!<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> 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.. <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> Best,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> Philipp <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> >>> Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> 18.06.2020 01:15 >>><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> Hi Philipp,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> This works fine for me using the menu. For example, start ChimeraX, then:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> open 2gbp<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> menu: Select... Structure... Secondary Structure... Strand<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> menu: Select... Define Selector... (I gave it the name "mystrands")<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> menu: Select... Clear<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> menu: Select... Structure... Ligand<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> menu: Select... Menu Mode... Add<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> menu: Select... User-Defined Selectors... mystrands<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> 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.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> Tested in version 1.0.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> I hope this helps,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> Elaine<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> -----<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> Elaine C. Meng, Ph.D. <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> UCSF Chimera(X) team<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> Department of Pharmaceutical Chemistry<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> University of California, San Francisco<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> > On Jun 17, 2020, at 1:11 PM, Philipp Milkereit <<a href="mailto:philipp.milkereit@vkl.uni-regensburg.de">philipp.milkereit@vkl.uni-regensburg.de</a>> wrote:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> ><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> > Dear all,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> > <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> > 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.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> > <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> > Many thanks for your help,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> > <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Segoe UI",sans-serif'>> > Philipp Milkereit<o:p></o:p></span></p></div></div></div></div></div></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>_______________________________________________<br>ChimeraX-users mailing list<br><a href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX-users@cgl.ucsf.edu</a><br>Manage subscription:<br><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><o:p></o:p></p></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>