Hi Thomas, Engin, Thanks for looking into this. Another thing with Select is that in this Pi version there is a "delete everything" option, which is very dangerous (it does delete every single object). It used to be "remove atoms" to remove only the atoms in the selection.
Best regards, Istvan On Thu, Mar 20, 2025 at 8:59 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 Also delete selection has been replaced by delete selections.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 > > _______________________________________________ > 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
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