Re: [PyMOL] Pymol not opening files

Thanks. I will try that. On Sun, 25 Feb 2024, 07:08 Jared Sampson, wrote: > Hi Shivani - > > PyMOL's defer_builds_mode > setting can improve > performance when loading large trajectories. > > You can type `set defer_builds_mode, 3` on the PyMOL

Re: [PyMOL] Pymol not opening files

I would not use pymol for big trajectory analysis. On Fri, 23 Feb 2024 at 22:13, shivani godbole wrote: > Hello, > > This is Shivani Godbole. I use Pymol for the movie files generated using > MD simulations. I am trying to use Pymol to visualize one of the movie > files which is around 2 GB in

Re: [PyMOL] Writing a trajectory file

Hi. I doubt it. I also would say that mdanalysys or pytraj will be better for big trajectories. If trajectory is big, Pymol will struggle. Petro. On Mon, 4 Dec 2023, 17:06 Istvan Kolossvary, wrote: > Hi, I was wondering, does Pymol have a way to save a trajectory directly > in .dcd, .xtc

Re: [PyMOL] centerofmass command gives error

Thanks. Yes it helps. On Tue, 23 May 2023 at 15:21, Jared Sampson wrote: > Hi Petro - It looks like that structure has a deuterium atom. Assuming > you're interested in the non-deuterated molecule, you can convert it to a > hydrogen and the command will work. > > ``` >

[PyMOL] centerofmass command gives error

Hi everybody I get the following error when I try to use center of mass commanand. Any Idea what is wrong? Thanks. Petro. --KeyError Traceback (most recent call last) Cell In[4], line 4 2

Re: [PyMOL] [EXTERNAL] Generate electrostatics by Python command

Hi Blaine. Thank you for your reply. I was not clear. I meant the surface which can be generated via action -> generate -> vacuum electrostatic -> protein contact potential (local) Is there a way to access it via Python? Thank you and best regards. Petro. On Wed, 17 May 2023 at 17:3

Re: [PyMOL] Surface and cartoon transparency together?

Thanks. I will try it. Best regards. Petro. On Wed, 17 May 2023 at 19:49, Jarrett Johnson < jarrett.john...@schrodinger.com> wrote: > Hi Petro, > > You might have luck using Order Independent Transparency: > > `set transparency_mode, 3` > > Hope that helps, > Jarr

Re: [PyMOL] [EXTERNAL] Disable cartoon representation on load

Thank you. I will try that. Best regards. Petro. On Wed, 17 May 2023 at 17:17, Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> wrote: > Hi Petro, > > Add the following to your .pymolrc file (pymolrc.pml on Windows) > > cmd.do("hide cartoon") > cmd.do(&qu

[PyMOL] Generate electrostatics by Python command

Hi. How can I generate electrostatics using Python API? Thanks. Petro. ___ 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

[PyMOL] Surface and cartoon transparency together?

HI., I have tried to use surface and cartoon transparency together but then I can see only the surface. Cartoon disappears completely. Any trick to get it working? Thanks, Petro ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol

[PyMOL] Disable cartoon representation on load

Hi. How can I force pymol to show things in lines, not in cartoons, by default? Thanks. Petro. -- __ Petro Khoroshyy ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] Connect to remote pymol instance.

the local computer? Thanks. Petro. ___ 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] Get/edit molecule title?

Hi Jared. Have not tried yet, but it looks like you have solved the problem for me. Thanks. Petro. On Thu, 19 Jan 2023, 8:13 pm Jared Sampson, wrote: > Hi Petro - > > This is the object's "title" attribute, and can be accessed using the > Properties > Inspector &l

Re: [PyMOL] Get/edit molecule title?

Hi again. I got a proposal to use the action menu, but it is a bit different. https://photos.app.goo.gl/GkCyr67JfWSDKUU57 Please take a look at this photo. I am interested in reading and editing the information in green. Thanks. Petro. On Wed, 18 Jan 2023 at 13:44, Petro wrote: > Hi, l

[PyMOL] Get/edit molecule title?

Hi, list. When I load the mol2 file, the title of the molecule is shown near the object name in green in the internal GUI. Is there a way to read it? Maybe even edit it? Thanks. Petro. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com

[PyMOL] Loading gromacs and amber trajectory

Hi. Is there a way to load gromacs and amber trajectory? Thanks Petro ___ 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

[PyMOL] About PostScript?

Dear All. Is it possible to save picture in vector postscript format? Thanks. Petro __ Do you Yahoo!? New and Improved Yahoo! Mail - Send 10MB messages! http://promotions.yahoo.com/new_mail