Hello Everyone, We have just released PyMOL 3.1.4.1 (which is still a digit of pi so the pi mole remains!) to fix the issues discussed in this thread.
Please give this version a try if you haven't updated recently since many other small issues have also been fixed in recent patches. You can download this version from the website ( https://www.pymol.org/#download) and please check back later if 3.1.4.1 isn't showing up for you yet. Release Notes: - Selection names are now properly shown within parentheses again (i.e. “(sele)”) - Fix for selections using the incorrect “Action” menu - Wizards that require keyboard input now focus properly - Fix for timeline extending off the edge of smaller Mac screens - Fix for issues toggling objects after reordering - Fix for group members not showing following an empty group Thank you for your patience and happy PyMOL-ing, Thomas Thomas Stewart | Senior Developer I | Product Manager, PyMOL [image: Schrödinger, Inc.] <https://schrodinger.com/> On Thu, Mar 20, 2025 at 8:42 PM Engin Özkan <eoz...@uchicago.edu> wrote: > Dear Thomas, > > Thank you for getting back quickly and on your work on PyMOL. Looking > forward to testing the patched version. > > Best, > > Engin > > > On 3/20/25 9:44 AM, Thomas Stewart wrote: > > Hello Engin and Vaheh, > > Both of these are simply oversights on my part and will be fixed in the > next patch (3.1.4.1). For this update, I completely rewrote the code for > the Contents Panel and there appears to be certain ASHLC menus that are not > pulling the correct set of menu options for their object type. > > I will also add the parentheses back to the selections! I'm honestly > surprised I didn't immediately notice this in my testing but it should be a > quick fix. > > Thank you for reporting these issues and let me know if you find anything > else. > > Thanks again, > Thomas > > Thomas Stewart | Senior Developer I | Product Manager, PyMOL > > [image: Schrödinger, Inc.] <https://schrodinger.com/> > > > On Thu, Mar 20, 2025 at 9:08 AM Oganesyan, Vaheh < > vaheh.oganes...@astrazeneca.com> wrote: > >> To add a bit to Engin’s message: under A when selecting “extract” I’m >> getting “copy” instead. I think it is a bug in 3.1.4. >> >> >> >> Thank you. >> >> >> >> Vaheh >> >> >> >> *From:* Engin Özkan <eoz...@uchicago.edu> >> *Sent:* Wednesday, March 19, 2025 8:02 PM >> *To:* pymol-users@lists.sourceforge.net >> *Subject:* [PyMOL] PyMOL 3.1.4 >> >> >> >> Hi, >> >> In the latest version of PyMOL, 3.1.4, I cannot see if an item in the >> list on the right-hand column is a selection or an object. The >> parantheses were really useful before. Is this intentional or an >> oversight? >> >> But more urgently, for a selection I made, I no longer see the options >> under "A" many options I use every session, such as copy to object, >> extract object, rename selection, align, etc. I am sure I can do these >> actions via command-line just fine, but not nearly with the same ease of >> use. >> >> Also delete selection has been replaced by delete selections. Why >> plural? I am scared to click on it, especially now that I don't know >> which items are selections and which are objects. I'll downgrade for now >> to be able to use selections effectively in PyMOL; I assume many users >> also depend on their ability to modify, align and rename selections >> easily. >> >> (And thanks for fixing some of the selection group bugs that popped up >> with v. 3 early on.) >> >> Best, >> >> Engin >> >> -- >> Engin Özkan, Ph.D. >> Associate Professor >> Dept of Biochemistry and Molecular Biology >> University of Chicago >> >> >> >> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> ------------------------------ >> >> *Confidentiality Notice: *This message is private and may contain >> confidential and proprietary information. If you have received this message >> in error, please notify us and remove it from your system and note that you >> must not copy, distribute or take any action in reliance on it. Any >> unauthorized use or disclosure of the contents of this message is not >> permitted and may be unlawful. >> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> > -- > Engin Özkan, Ph.D. > Associate Professor > Dept of Biochemistry and Molecular Biology > University of Chicago > Phone: (773) 834-5498http://ozkan.uchicago.edu > >
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