Re: [PyMOL] PyMOL 3.1.4

[Thomas S. <tho...@sc...>]

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 <eo...@uc...> 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 <
> vah...@as...> 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 <eo...@uc...>
>> *Sent:* Wednesday, March 19, 2025 8:02 PM
>> *To:* pym...@li...
>> *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/pym...@li...
>> 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/pym...@li...
>> 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
>
>