Re: [PyMOL] Viewing PyMol in 3D
Hi PyMOLers We recently bought Asus V278H monitors, which displays nice stereo under Linux (Ubuntu 12.04). The monitors were bundled with Nvidia 3D vision v2 glasses. We have Quadro FX5800 cards, but we do NOT use the 3-pin stereo port, but rather the built-in emitter in the monitors. I have pasted my notes from the installation below. Is works with PyMOL as well as other OpenGL applications, such as VMD, Accelrys Discovery studio, CCDC GOLD/Hermes, Yasara, etc. Cheers, Esben Asus VG278H flat panel 3D screens and Ubuntu 12.04 These screens have built-in emitters that actually work under Linux, with Nvidia drivers version 310 or newer. (These drivers are packaged in Ubuntu 12.04, so they're easy to install) Install by closing X and install: sudo service lightdm stop use Ctrl-Alt-F1 to swith to a text console and login (possibly, but not strictly necessary) as root wajig install nvidia-experimental-310 /etc/lightdm/lightdm.conf This file is very important for geting the right video mode for the login screen (via the script in /etc/X11/set_1920x1080.sh, otherwise the X-server doesn't start at all). It also makes sure that the username has to be typed instead of selected from a list (very important when the system has many users) [SeatDefaults] user-session=ubuntu greeter-session=unity-greeter greeter-show-manual-login=true greeter-hide-users=true display-setup-script=/etc/X11/set_1920x1080.sh session-setup-script=/etc/X11/set_1920x1080.sh /etc/X11/set_1920x1080.sh This script calls the xrandr tool to set the videomode #!/bin/bash xrandr --output DVI-I-3 --mode 1920x1080 --rate 120 Note!! It seems that when everything is installed, there are still some tweaks to do (not completely sure though) * Reboot * For stereo to work the first time, I had to stop lightdm (see above), switch to a text console and login as normal user, then do startx to start the X-window system. Now check if stereo works. If so, then switch back to the text console and kill the X-server (Ctrl-C). The restart lightdm and login from the graphical login screen. Then it should work. /etc/X11/xorg.conf I dont know how important the xorg.conf file actually is, but here's my copy # nvidia-xconfig: X configuration file generated by nvidia-xconfig # nvidia-xconfig: version 310.14 (buildmeis...@swio-display-x86-rhel47-06.nvidia.com) Tue Oct 9 13:04:01 PDT 2012 Section ServerLayout Identifier Layout0 Screen Screen0 InputDeviceKeyboard0 CoreKeyboard InputDeviceMouse0 CorePointer EndSection Section Files EndSection Section InputDevice # generated from default Identifier Mouse0 Driver mouse Option Protocol auto Option Device /dev/psaux Option Emulate3Buttons no Option ZAxisMapping 4 5 EndSection Section InputDevice # generated from default Identifier Keyboard0 Driver kbd EndSection Section Monitor Identifier Monitor0 VendorName Unknown ModelName Unknown HorizSync 28.0 - 400.0 VertRefresh 43.0 - 120.0 Option DPMS EndSection Section Device Identifier Device0 Driver nvidia VendorName NVIDIA Corporation EndSection Section Screen Identifier Screen0 Device Device0 MonitorMonitor0 DefaultDepth24 Option NoPowerConnectorCheck True Option UseEdid True Option ModeDebug True Option Stereo 10 Option 3DVisionDisplayType 1 SubSection Display Depth 24 EndSubSection EndSection Section Extensions Option Composite Disable EndSection Best Regards Esben Peter Friis Science Manager Novozymes A/S Krogshoejvej 36 2880 Bagsvaerd Denmark Phone: +45 44461334 Mobile: +45 30771334 E-mail: e...@novozymes.com --- Don't print today - contribute to a better environment tomorrow --- Novozymes A/S (reg. no.:10007127). Registered address: Krogshoejvej 36 DK-2880 Bagsvaerd, Denmark This e-mail (including any attachments) is for the intended addressee(s) only and may contain confidential and/or proprietary information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information herein is strictly prohibited. If you are not an intended recipient you should delete this e-mail immediately. Thank you. From: Max Ferretti [mailto:mferr...@scripps.edu] Sent: 10. december 2012 17:22 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Viewing PyMol in 3D Hey everyone, Does anyone have experience setting up pymol to be viewed in 3D with glasses? I'm hoping to build a system for this purpose. From what I have read, I will need a recent NVidia Quadro card and a 3D-capable LCD monitor with a resolution of at least 120Hz. I'm not sure if I need
[PyMOL] Delete empty objects
Hello, Is there a quick way to delete the objects that do not contain any atoms? Thank you in advance, Vitaly -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Delete empty objects
Hi Vitaly, Try for i in cmd.get_object_list(): cmd.get_model(i).get_coord_list() or cmd.delete(i) Ciao! Tsjerk On Tue, Dec 11, 2012 at 9:31 AM, V.V. vvos...@gmail.com wrote: Hello, Is there a quick way to delete the objects that do not contain any atoms? Thank you in advance, Vitaly -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] alignto command
is there a way of getting the alignto command to print out RMS deviations over the aligned regions of the structures. thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] make bond between two atoms
Hena, I created two objects as follows: pseudoatom A1, pos=[10.0, 10.0, 100.0] pseudoatom A2, pos=[10.0, 10.0, -200.0] I want to create a bond between these two atoms. Could you please help me? I need to display a 2 fold axis passing through these points. You can create a distance measure between them as shown here, http://www.pymolwiki.org/index.php/Pseudoatom. Or you can do this: pseudoatom foo1, pos=[0,0,0], name=CA pseudoatom foo2, pos=[1,1,1], name=CB create foo, foo1 or foo2 bond fooCA, fooCB which creates a single object from the two pseudoatoms and bonds the two pseudoatoms. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Help with alignments
I am wanting to align proteins based on superposition of particular chains. Is it possible to do the superposition based on the chains, but to move, in this case the entire complex ??? Thanks Jon Sent from my iPad -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Help with alignments
Hi Jon, align prot1 and chain A, prot2 and chain X 'super' and 'cealign' should work similarly. Cheers, -- Jason On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes jonat...@strubi.ox.ac.uk wrote: I am wanting to align proteins based on superposition of particular chains. Is it possible to do the superposition based on the chains, but to move, in this case the entire complex ??? Thanks Jon Sent from my iPad -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Help with alignments/ more general create and align question
I don't want to hijack the thread but I was curious if you can point to few pymol features for generating and rotating molecules and how they would play with other tools. For example, if I just go download pdb files or take output from DFT, it may be easier to do analysis with certain alignments. Similarly, I want to generate hypothetical molecules for various tests and wanted some easy way to do that. There are many graph, shape, or geometry tools available in various fields, maps, CAD etc and apparently they are tools for drawing or editing molecules. However, I was just looking for something that works from command line and is reasonably easy to integrate with other things. Apparently pymol is all based on python and presumably features, like the plugins you pointed me to earlier, are easy to mix and match with other tools but not sure offhand how to approach this. Right now, I'm making my own c++ tool using Tcl front end so that I can eventually use all the math libraries like lapack and boost as I want to do larger molecules( and use these for various types of alignments that could generate large matricies ). Should I use python or just use something that pymol already has? The immediate need is just to generate xyz files that look like short polyenes and be able to perturb them using a script. So for this I end up with Tcl input that looks like a list of atom and direction commands but there is probably some way to do this much with existing tools. Thanks. From: jason.vertr...@schrodinger.com Date: Tue, 11 Dec 2012 07:38:32 -0600 To: jonat...@strubi.ox.ac.uk CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Help with alignments Hi Jon, align prot1 and chain A, prot2 and chain X 'super' and 'cealign' should work similarly. Cheers, -- Jason On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes jonat...@strubi.ox.ac.uk wrote: I am wanting to align proteins based on superposition of particular chains. Is it possible to do the superposition based on the chains, but to move, in this case the entire complex ??? Thanks Jon Sent from my iPad -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
