Re: [PyMOL] Running pymol without launching window in batch

Hello, It is much easier than that. Make a pymol script, for example, test.pml: # load 3gbn.pdb select Selection1, resi 80:115 save Selection1.cif, Selection1 quit # then run it with the -c option : pymol test.pml -c If you want to pass an argument, like the filename of a pdb file to be dire

Re: [PyMOL] Solid stick between two residues?

> On 5 Sep 2022, at 16:39, Bruhn, Matthias wrote: > > Dear pymol users, > does anybody recognize this type of bond and can explain me what this is? It > appears between a Lysine and an Aspartic acid. I expect a hydrogen bond, but > for some reason PyMol connects the two amino acids with a sti

Re: [PyMOL] How to show orientation axis in Pymol

Hi, Quite easy using CGO : https://pymolwiki.org/index.php/Cgo_arrow Florian > On 23 Jun 2022, at 14:40, Gundala Viswanath wrote: > > Hi, > > Is there a way to show the orientation axis in Pymol? > VMD can do this: > > > > > G.V. > __

Re: [PyMOL] PyMOL for M1 macs

Hi, You can install the open source version 2.5 of PyMOL using homebrew and it will be M1 native (see https://brew.sh) But frankly, the intel version is already so fast with rosetta2 on the M1 that it does not worth it except if you do really fancy stuff. Florian > On 6 Dec 2021, at 08:00, Ch

[PyMOL] Pymol in conda-forge osx-arm64 for new M1 Macs

Hello, I want to install a native version of Pymol for the new M1 Mac with conda but Pymol is not yet in the new osx-arm64 platform in conda-forge (https://conda-forge.org/blog/posts/2020-10-29-macos-arm64/ ) Is there any work to put

[PyMOL] Mapping picture to CGO object in PyMOL?

Hi, Probably a fancy request, but is there any way to map a picture to a cgo object in PyMOL, like a plane or a sphere? Best, Florian -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover t

Re: [PyMOL] rendering issue, stick mode, MacBook Pro Retina MacOS 10.8.2.

On 14 oct. 2012, at 17:37, Jason Vertrees wrote: > Florian, > > If you turn off stick_use_shader you will get slower and less pretty on > screen rendering. I suggest keeping that one enabled. > > Cheers, > > Jason Thank you for the suggestion, I actually followed your workaround as soon as

Re: [PyMOL] rendering issue, stick mode, MacBook Pro Retina MacOS 10.8.2.

On 14 oct. 2012, at 15:59, Jason Vertrees wrote: > Florian, > > This is a bug with OS X 10.8 and later. It also appears on some different > combinations of hardware. Anyhow, the fix is easy, and this will be > automatically fixed in our next release: > > set cylinder_shader_ff_workaround, 1

[PyMOL] rendering issue, stick mode, MacBook Pro Retina MacOS 10.8.2.

Hi, I have a weird rendering issue on a MacBook Pro Retina. See this image (http://i45.tinypic.com/34xjsoz.png). This problem exist with the 1.5.0 and 1.5.4 versions of pymol. The stick representation becomes completely invisible when switching to white background. Ray tracing is fine though.

Re: [PyMOL] Using Volumes

On 12 sept. 2011, at 14:20, Jason Vertrees wrote: > Greetings, > > One chance encounter at ACS couple weeks ago turned into a multi-day > discussion about using the new volume visualization for presenting > field data. Leroy Laverman from UCSB now has some example movies > showing how the electr

Re: [PyMOL] PyMOL on the Mac

On 20 Jan 2010, at 22:07, Jason Vertrees wrote: > PyMOLers, > > I just want to quickly reiterate: PyMOL will still be supported on the > Mac--no need to worry. Even though other Schrodinger software doesn't > run on the Mac, PyMOL will. Actually, I expect that schrodinger will port their own s

Re: [PyMOL] Autodock/Vina Pymol Plugin Windows problem

On 8 Jan 2010, at 09:51, Daniel Seeliger wrote: > > Btw, did anyone get it to run on windows or mac? If yes, it would be nice if > you drop me a mail with some info about your system (operating system, > program > version, how is pymol installed). Hi Daniel, The plug-in works great on a Mac

[PyMOL] blue line stereo on a MacBook

Hi, I'm trying to get blue line stereo on my MacBook pro (OS X.4.10 Radeon X1600) It is connected to a 21" SGI CRT monitor (1024x...@120hz). I launched pymol 0.99rc6 using /Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL -B -X -1000 to force Blue line stereo and opening of PyMol on t

Re: [PyMOL] PowerbookG4 z-screen stereoenabler

only way to get stereo-in-a-window (Quad buffer). But full screen stereo should work with the stereoenabler using the blue line code. -- Florian NACHON, phD CRSSA Grenoble, France "Every man has two nations, and one of them is France" Benjamin Franklin & Thomas Jefferson

[PyMOL] PowerbookG4 z-screen stereoenabler

ppreciated, Thanx -- Florian NACHON, phD CRSSA Grenoble, France "Every man has two nations, and one of them is France" Benjamin Franklin & Thomas Jefferson

[PyMOL] Interface for native OS X version.

On 3 nov. 03, at 22:29, pymol-users-requ...@lists.sourceforge.net wrote: 2)The interface for mac is .. well.. very uncomfortable. Is there a chance of improvement soon? What exactly do you mean? I guess Einat talks about the tk interface that is missing in the native OS X version of PyMol.

[PyMOL] PyMol 0.92 via fink

Hi Warren, When will PyMol 0.92 be available via fink? Thanks, Scott I wrote an email to Matt Stephenson who is the package maintainer. Hope he will reply soon. If you want to write him yourself, his email is catt...@users.sourceforge.net Florian

Re: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window

On 24 oct. 03, at 11:59, Warren L. DeLano wrote: Florian, The main trick is to use an X11/Fink build of PyMOL. Under 10.3, I'm hoping OpenGL performance under X11 will be more that of the native version -- any early returns on this yet? I'm using Panther and it seems that the OpenGL performa

Re: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window

On 24 oct. 03, at 11:59, Warren L. DeLano wrote: Florian, The main trick is to use an X11/Fink build of PyMOL. Under 10.3, I'm hoping OpenGL performance under X11 will be more that of the native version -- any early returns on this yet? I'm using Panther and it seems that the OpenGL performa

Re: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window

On Oct 22, 2003, at 8:42 PM, pymol-users-requ...@lists.sourceforge.net wrote: Tkinter is a separate Python module that's an interface to the Tcl Tk library. It's probably just not installed on your system, but it is included in the RH 9 distribution (tkinter-2.2.2-26.i386.rpm) so it should b

[PyMOL] Re: PyMOL-users digest, Vol 1 #264 - 4 msgs

On Monday, Feb 3, 2003, at 14:12 America/Chicago, pymol-users-requ...@lists.sourceforge.net wrote: Best Uwe Hobohm PS: Poor Mac-Users would like support for their one-button mouses (minority request...) The Poor Mac Users should buy a 3 buttons mouse like the optical wheelmouse from log

[PyMOL] Re: PyMOL-users digest, Vol 1 #257 - 2 msgs

On Wednesday, Jan 22, 2003, at 14:05 America/Chicago, pymol-users-requ...@lists.sourceforge.net wrote: On Wednesday, January 22, 2003, at 10:38 AM, wgsc...@chemistry.ucsc.edu wrote: Are you using OS 10.2.3? You won't derive the benefits of the acceleration unless you have 10.2.3. Beyond th

[PyMOL] Latest Apple G4 graphic cards and PyMOL (Luca Jovine)

On Monday, Sep 23, 2002, at 14:06 America/Chicago, pymol-users-requ...@lists.sourceforge.net wrote: Dear OSX PyMOL users, I'd like to hear about your experience with PyMOL using either of the graphic cards shipping with the latest Apple G4s (ATI Radeon 9000 Pro card 64 DDR and NVIDIA GeForce4

Re: [PyMOL] Pymol slow on a mac G4 with os 10.1

Russell Poyner wrote: The machine is a newish G4 733Mhz 256K ram with a radeon 7500 card. I have installed the Fink version of pymol with the Fink supplied Xfree. It works but is noticably slower than pymol on my 500 Mhz K6/lintel box, also with a radeon 7500 and Xig xserver. It would see

Re: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX

-in drivers for multi-button mice. It supports the 3 buttons + the wheel. I'm still wondering why Apple is not selling multi-button mice with their computers... Bye -- Florian NACHON, phDCRSSA Grenoble, France - UNMC Omaha, USA "Every man has two nations, and one of them is Fr