[PyMOL] PyMOL crashes when building a nanotube
Hi, I'm building a nanotube by adding some polymer side chains to a nanotube that I already have (pdb files). I've been able to do about 1/2 of adding the side chains but now when I open the pse file or the saved project as a pdb to continue editing it, PyMOL crashes as soon as I open the builder tool. I get a pop up before the builder tool is loaded saying: "Building "Undo" is disabled for the following objects nanotube Enable "Undo" for these objects? No/Yes" I've tried both options (working after clicking "No" and after "Yes") and PyMOL still crashes. Any suggestions as to how to fix this? I have a grant proposal deadline coming up and this novel molecule is the subject of that proposal. Sincerely, Vy *Vyshnavi Karra (she/her/hers) * *Ph.D Student, Northeastern University * *M. Sc. Chemical Engineering, Rutgers University (2017) * *B. S. Chemical Engineering, Rutgers University (2016) * *Email: karr...@husky.neu.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
Re: [PyMOL] How to compile pymol with --glut?
Hi Yeping, This has been asked before (by you :-)), see here: https://sourceforge.net/p/pymol/mailman/message/36766620/ Cheers, Thomas > On Feb 8, 2020, at 2:12 PM, 孙业平 via PyMOL-users > wrote: > > Dear pymol users, > > I compiled pymol following the guide at > https://pymolwiki.org/index.php/Linux_Install in my CentOS 8 system. > When I tried to launch pymol by the "./pymol" command, I got the following > error: > > Qt not available, using GLUT/Tk interface > Traceback (most recent call last): > File > "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", > line 65, in > pymol.launch(args) > File > "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", > line 441, in launch > _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook) > NotImplementedError: compile with --glut > > I then removed the "bin" and the "lib64" directories in the > "pymol-open-source-build" directory and recompiled pymol with the following > command: >python3 setup --glut install > --prefix=~/software/Pymol/pymol-open-source-build > > However, the newly generated pymol binary file does not work either. Launch > pymol give the same "Qt not available, using GLUT/Tk interface" error. > > Could you help me with this?Thank you in advance. > > Best regards. > > > ___ > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ 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
Re: [PyMOL] floating external gui
Hi Tamas, It is currently not possible to start PyMOL with a floating external GUI. The most convenient way to get it floating is to double click the empty space of the panel which toggles visibility of its title bar, then drag that out. See attached screenshot. Cheers, Thomas > On Feb 8, 2020, at 10:56 AM, Tamas Hegedus wrote: > > Hi, > > I am using a compiled version of pymol. > I like the floating window. > > The CNTR-E does not work to toggle floating, I have to use the mouse > (display, external gui, toggle floating). > Is it possible to start pymol with floating external gui? > > Thanks, Tamas > > ___ > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ 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
Re: [PyMOL] Getting session file name
Hi Jason,
This should do it:
name = cmd.get('session_file')
Cheers,
Thomas
> On Feb 8, 2020, at 5:21 AM, Junsu Park aka. Jason Mosier
> wrote:
>
> Hello, this may be a very simple question that I just can't find the answer
> to, but I was wondering how I would go about fetching the session name of the
> .pse currently open? For example, I have two session files: colors and
> overlays, and I want my code to print something specific for each colors...
> and overlay... in a text file or whatever based on which one I have open
>
> Cheers,
> Jason M.
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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