Re: [PyMOL] stereo requirements
Hi Gary GeForce cards do support Nvidia 3D vision 2 under Windows, but in full screen only. (Tested with Windows 8, PyMOL and an Alienware 3D-capable laptop). If you need stereo-in-a-window, you must have a Quadro card. It works with Yasara too (full screen), but for unknown reasons, the stereo is not stable for the internal laptop 3D screen – it looses stereo sync after some time. An external 3D screen connected to the laptop works fine, though. Cheers, Esben 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.commailto:e...@novozymes.com Web: www.novozymes.comhttp://www.novozymes.com Follow Novozymes on: LinkedInhttp://www.linkedin.com/company/novozymes/ | Twitterhttps://twitter.com/Novozymes/ 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: Gary Hunter [mailto:gary.hun...@um.edu.mt] Sent: 1. juni 2015 10:09 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] stereo requirements To avoid confusion (mine) can you please specify whether or not Quadro cards are still necessary for stereo on Windows systems. Will a GeForce card (not quadro) support nvidia nvision 3D ? I remember a recent post concerning this but cant seem to find it. Gary Hunter -- Prof. Gary J. Hunter, Department of Physiology and Biochemistry University of Malta, Msida, MSD 2080, Malta. phone: +356 2340 2917 phone: +356 21316655 (secretary), Fax: +356 21310577 http://www.um.edu.mt/ms/physbiochem There may be confidential information within the contents of this email meant only for the person addressed. This email must not be forwarded to third parties without the express consent of the sender. If you believe you have received this email in error please inform the sender and remove it from your system. -- ___ 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] NVIDIA 3D error
I thought all quadro cards supported stereo? (must admit that I'm not sure :-) The 3 pin stereo connector is not needed to get stereo with the Asus monitors - they get the stereo sync via DVI. But the stereo mode 10 and/or 11 must be supported by the card and driver. My main problem was to force the card into 120hz mode, which required the xrandr utility. Without the xrandr command, I could only get the card to run 60 Hz, where stereo is not possible. Cheers, Esben Den 21/07/2013 kl. 09.17 skrev Harry Mark Greenblatt harry.greenbl...@weizmann.ac.ilmailto:harry.greenbl...@weizmann.ac.il: BSD It's not clear to me if the K600 card specified by Dick in his post will actually support stereo under Linux. It has no 3 pin stereo connector for the emitter, and I was under the impression that one could only get Stereo Mode 10 or 11 under linux using the Quadro cards with the stereo option (K5000, K4000, or legacy cards like FX 3700, FX 3800, etc.). Have things changed? Harry On Jul 19, 2013, at 10:51 PM, Davis, Malcolm wrote: 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: Richard Harper [mailto:drrwhar...@gmail.com] Sent: 19. juli 2013 00:52 To: pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net Subject: [PyMOL] NVIDIA 3D error I think I have tried all the solutions available. I continue to get: error: the requested 3d display mode is unavailable. I can run all the examples; apparently correctly. ASUS VG248 monitor NVIDIA quatro K600 video card NVIDIA 3D vision Suggestions? Dick - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenbl...@weizmann.ac.ilmailto:harry.greenbl...@weizmann.ac.il Weizmann Institute of SciencePhone: 972-8-934-3625 234 Herzl St.Facsimile: 972-8-934-4159 Rehovot, 76100 Israel -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ 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] NVIDIA 3D error
There is no way to make this work with Ubuntu 10.04 :-( The requires stereo modes 10 or 11 are only availble in newer Nvidia driver versions, which are not compatible with the older kernel in 10.04. We had to upgrade to 12.04 for that reason. Cheers, Esben Den 19/07/2013 kl. 21.51 skrev Davis, Malcolm malcolm.da...@bms.commailto:malcolm.da...@bms.com: This may be a red herring, but earlier this year we purchased several ASUS VG278H monitors and initially could not get even the glxgears -stereo demo to display in stereo. We checked all of our xorg.conf settings with NVidia and still no stereo. However, when we upgraded from RHEL5 to RHEL6 everything worked perfectly. One point of difference between our setup and the one quoted below is we have Stereo set to 10 and not 11. 11 is for VisionPro which uses RF instead of the IR emitters. Malcolm From: EPF (Esben Peter Friis) [mailto:e...@novozymes.com] Sent: Friday, July 19, 2013 2:50 AM To: Richard Harper; pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] NVIDIA 3D error Hi Dick A hint about your setup would be helpful :-) I Assume you use Linux. Our ASUS VG278H monitors works fine in 3D stereo with Nvidia Quadro FX5800 cards. I have pasted my notes about how I configured X. Cheers, Esben Asus VG278H flat panel 3D screens and Ubuntu 12.04 These screen 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 [edithttp://pd.novo.dk/mediawiki/index.php?title=Linux_workstationsaction=editsection=2] /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 [edithttp://pd.novo.dk/mediawiki/index.php?title=Linux_workstationsaction=editsection=3] /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 [edithttp://pd.novo.dk/mediawiki/index.php?title=Linux_workstationsaction=editsection=4] 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. [edithttp://pd.novo.dk/mediawiki/index.php?title=Linux_workstationsaction=editsection=5] /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.commailto: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 11 Option 3DVisionDisplayType 1 SubSection Display Depth 24 EndSubSection EndSection
Re: [PyMOL] NVIDIA 3D error
Hi Dick A hint about your setup would be helpful :-) I Assume you use Linux. Our ASUS VG278H monitors works fine in 3D stereo with Nvidia Quadro FX5800 cards. I have pasted my notes about how I configured X. Cheers, Esben Asus VG278H flat panel 3D screens and Ubuntu 12.04 These screen 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 [edithttp://pd.novo.dk/mediawiki/index.php?title=Linux_workstationsaction=editsection=2] /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 [edithttp://pd.novo.dk/mediawiki/index.php?title=Linux_workstationsaction=editsection=3] /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 [edithttp://pd.novo.dk/mediawiki/index.php?title=Linux_workstationsaction=editsection=4] 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. [edithttp://pd.novo.dk/mediawiki/index.php?title=Linux_workstationsaction=editsection=5] /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 11 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 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: Richard Harper [mailto:drrwhar...@gmail.com] Sent: 19. juli 2013 00:52 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] NVIDIA 3D error I think I have tried all the solutions available. I continue to get: error: the requested 3d display mode is unavailable. I can run all the examples; apparently correctly. ASUS VG248 monitor NVIDIA quatro K600 video card NVIDIA 3D vision
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
Re: [PyMOL] Sequence alignment editing
Hi Dimitry if you add an object=some name to your align command, then the sequences are shown correctly aligned. The residues used in the alignment are shown in their normal colors, the excluded onses are shown in gray, eg: align obj01CA, obj02CA, object=alignment I think you should be able to save the alignment by this command: save alignment.aln, alignment Best Regards Esben Peter Friis Research Scientist Novozymes A/S Krogshoejvej 36 2880 Bagsvaerd Denmark Phone: +45 44461334 E-mail: e...@novozymes.com 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. -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DimitryASuplatov Sent: 22. august 2008 12:40 To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Sequence alignment editing Hello, I have two structures of related organisms. I want to align them in 3D with pymol and be able to view their sequences aligned as well (corresponding to structure alignment). Right now when using Display-Sequence mode sequences are displayed simply 'as is' even after 3D 'align' command. Could something be done? Thanks. Thanks! SDA. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] 3D Glasses. Where to buy them ?
Hi Sabuj Do these only work for programs under Linux that specifically implement page flipping stereo? Yes. The application must support OpenGL stereo. I have tested with the following programs: - VMD - PyMOL - Accelrys InsightII - Accelrys DiscoveryStudio The software that they describe which must be installed seems to be only for Windows (which also gives you page flipping stereo on LCDs). They deliver some drivers, which is for Windows only. On Linux, You must use a stereo-enabled graphics card (ie. most Nvidia Quadro series, no cheap GForce cards). The edimensional glasses also comes with a break-out box to mount between the graphics card and the monitor. This cannot be used with Linux, but the IR-emitter fits directly in the stereo port on the graphics card. All the best Esben
Re: [PyMOL] 3D Glasses. Where to buy them ?
Hi David Try http://www.edimensional.com/. They have a UK sales office. We use those glasses with our Linux systems, and they work fine :-) /Esben Best Regards Esben Peter Friis Phone: +45 44461334 E-mail: e...@novozymes.com Novozymes A/S (reg. no.: 10007127) 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. -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of David McGiven Sent: 29. oktober 2007 11:36 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] 3D Glasses. Where to buy them ? Dear PyMol Users, I know this isn't strictly pymol related but I suppose there are other users interested on that. I've been trying to contact 3D Glasses dealers for the last months but have no luck. There's REALD and Nuvision 3D manufacturers, but they don't seem to reply emails. Strange. Has anybody bought glasses from them in the last months ? Specifically from Europe. Best Regards, David McGiven -- --- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Trouble making pictures in a script
Hi Michael If the system is very big and causes the ray tracing to crash, try to lower the hash_max setting. I think the default is 100. If the setting is lower, it will be slower, but use less memory. (and vice versa :-) All the best Esben -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano Scientific Sent: 25. oktober 2007 18:11 To: 'Michael Lerner'; 'pymol mailinglist' Subject: Re: [PyMOL] Trouble making pictures in a script Michael, The -c option forces PyMOL to run in command-line-only mode which means it doesn't have access to the OpenGL hardware (used by cmd.draw and interactive graphics). In command-line-only mode, ray tracing (cmd.ray) is the only option. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Michael Lerner Sent: Thursday, October 25, 2007 8:31 AM To: pymol mailinglist Subject: [PyMOL] Trouble making pictures in a script Hi, I have a Python script that sets a system up and then calls cmd.png() to render an image. I use it to process several files at a time, and there's no need to look at it while it's working, so I use pymol -qcr myscript.py to launch it. It works fine when I ray trace things, but if I just set the system up and call cmd.png(), I get this error: ScenePNG-WARNING: invalid context or no image. Calling cmd.draw() instead of cmd.ray() doesn't seem to fix things. Any ideas? Some of the systems are big enough that cmd.ray() fails, so I'd like to be able to find a workaround. Thanks, -michael -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner -- --- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- --- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] questions
Hi Chandra If the sequences have some similarity, it is no problem :-) align structure1 and chain B and name CA, structure2 and chain C and name CA All the best Esben -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Chandra Verma Sent: 21. marts 2007 01:58 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] questions Hi if i have two structures loaded in pymol with structure 1 consisting of chains A and chain B of different sequences and similarly structure 2 consisting of chains C and D is it possible to superpose chain B of structure 1 onto chain C of structure 2? thanks chandra -- --- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforge CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Cutaway surfaces
Hi Rob A bit confusing :-) But the trick in such cases is usually to duplicate your object, and show the cutaway surface on the original and the cartoon/helix/etc on the copy. The cutaway surface is often easier to create by box-selecting (with the mouse) everything but the part that should be left open, and then show surface of the selection Also confusing? :-) Cheers Esben On Wed, 2006-08-02 at 15:30, Robert Court wrote: Hi. I want to make a figure showing a cutaway surface representation of a large complex showing a channel containing a peptide helix. If I show the surface and cartoon representations respectively and fiddle around with the clipping and slabing I can't get it so that the channel is 'open' without clipping part of the helix. Is it possible to make an image of the cutaway surface and superimpose the helix? Sorry if that's confusing! Cheers, Rob - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Putty
Hi Elo
The formula for cmputing the putty radius is found in layer1/ Extrude.c
in the source:
switch(source_field) {
default: /* b*/
scale = (range+(at-b - mean)/stdev)/range;
if(scale0.0F)
scale = 0.0F;
scale=(float)pow(scale,power);
if(scalemin_scale)
scale=min_scale;
if(scalemax_scale)
scale=max_scale;
*sf = scale;
break;
From this I can see:
* The cartoon_putty_scale_max and cartoon_putty_scale_min settings
are not scaling factors, but rather cut-off values to avoid extremely
thin or thick tubes.
* cartoon_putty_scale_power is a kind of gamma correction which
allows to enhanche areas with extreme b-factors. Set it to 1 if you want
linear scaling to b-factor.
* cartoon_putty_range is the only user-adjustable parameter that
affects the actual scaling.
* The mean value and standard deviation of the b-factors is used for the
scaling. This seems very strange to me - is this a bug or a feature? :-)
It is quite hard to make a workaround (without changing the source).
The best I could find was to combine all the (aligned) structures into
one object, but with different chainid, eg
alter obj01, chain='A'
alter obj02, chain='B'
create comb, obj01+obj02
Then make the putty cartoon
show cartoon, comb# Notice that the complete object must be
selected, the putty scaling works only on the displayed atoms!
cartoon putty, comb
But then your putty cartoons of the different structures are - at least
partly - covering each other. Then translate the different chains to
create the view you want, eg:
translate [20, 0 0 ], comb and chain A
You can use this view directly, or just translate the unwanted chains
far enough to be off the screen
Hope this helps :-)
But I I would really like an option to do manual scaling on the putty
cartoon, eg by changing the source line to.
scale = at-b * cartoon_putty_myscaling;
Where cartoon_putty_myscaling is a new setting.
Cheers,
Esben
Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Caspar
Elo Christensen
Sent: 24. juli 2006 22:24
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Putty
Hi,
I'm using cartoon putty to display rmsd between an enzyme with
and without ligand. I've got two enzymes (that is four structures all in
all) and have prepared two figures. The problem is that the extreme rmsd
values vary; in one figure it goes from 0.1 to 1.66 while in the other
it goes from 0.1 to 2.33. It seems that the rmsd values are normalized
by putty, so that the figures only allow me to compare the distribution
of rmsd values in each set of structures, not the actual values.How do I
put the two figures on the same scale, so that I can compare them
quantitatively?
I've tried to play around with the scale range parameters with
little luck.
Any help will be much appreciated,
Elo
Re: [PyMOL] Putty
Hi Elo
The formula for cmputing the putty radius is found in layer1/ Extrude.c
in the source:
switch(source_field) {
default: /* b*/
scale = (range+(at-b - mean)/stdev)/range;
if(scale0.0F)
scale = 0.0F;
scale=(float)pow(scale,power);
if(scalemin_scale)
scale=min_scale;
if(scalemax_scale)
scale=max_scale;
*sf = scale;
break;
From this I can see:
* The cartoon_putty_scale_max and cartoon_putty_scale_min settings
are not scaling factors, but rather cut-off values to avoid extremely
thin or thick tubes.
* cartoon_putty_scale_power is a kind of gamma correction which
allows to enhanche areas with extreme b-factors. Set it to 1 if you want
linear scaling to b-factor.
* cartoon_putty_range is the only user-adjustable parameter that
affects the actual scaling.
* The mean value and standard deviation of the b-factors is used for the
scaling. This seems very strange to me - is this a bug or a feature? :-)
It is quite hard to make a workaround (without changing the source).
The best I could find was to combine all the (aligned) structures into
one object, but with different chainid, eg
alter obj01, chain='A'
alter obj02, chain='B'
create comb, obj01+obj02
Then make the putty cartoon
show cartoon, comb# Notice that the complete object must be
selected, the putty scaling works only on the displayed atoms!
cartoon putty, comb
But then your putty cartoons of the different structures are - at least
partly - covering each other. Then translate the different chains to
create the view you want, eg:
translate [20, 0 0 ], comb and chain A
You can use this view directly, or just translate the unwanted chains
far enough to be off the screen
Hope this helps :-)
But I I would really like an option to do manual scaling on the putty
cartoon, eg by changing the source line to.
scale = at-b * cartoon_putty_myscaling;
Where cartoon_putty_myscaling is a new setting.
Cheers,
Esben
Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Caspar
Elo Christensen
Sent: 24. juli 2006 22:24
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Putty
Hi,
I'm using cartoon putty to display rmsd between an enzyme with
and without ligand. I've got two enzymes (that is four structures all in
all) and have prepared two figures. The problem is that the extreme rmsd
values vary; in one figure it goes from 0.1 to 1.66 while in the other
it goes from 0.1 to 2.33. It seems that the rmsd values are normalized
by putty, so that the figures only allow me to compare the distribution
of rmsd values in each set of structures, not the actual values.How do I
put the two figures on the same scale, so that I can compare them
quantitatively?
I've tried to play around with the scale range parameters with
little luck.
Any help will be much appreciated,
Elo
RE: [PyMOL] run out of memory problem
If the Mac version has the option hash_max, try to decrease it. The rendering will take longer, but the memory usage will be lower. For example: set hash_max, 50 Try with different values. I think the default is 100. Best wishes Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of matthew.frank...@imclone.com Sent: 27. april 2006 03:03 To: XIE, DONGLU Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] run out of memory problem pymol-users-ad...@lists.sourceforge.net wrote on 04/26/2006 08:03:40 PM: Hi all, The binary distribution (macpymol-0_99rc6.tar.gz) of PyMol 0.99 was installed in Mac 10.4.6. This Mac has 1.5G memory. When doing ray, it was using about 1.2G memory, it stopped in the middle and at last it died. The error message is about running out of memory. Did anybody meet the same problem? Thanks. -Donglu Hi Donglu - We need more information to figure out what happened. How much memory was Pymol using when you first launched it? What about right before you started the raytracing? Are you rendering an unusually large or complex image? You can try adjusting the memory settings for raytracing: in the Setting menu, go to Rendering then Memory. Try the various options and see if you still run out of memory. If your image is complex, try reducing the quality. In the Display menu, go to Quality. You may be able to reduce the quality a bit without noticeably affecting the image and it should reduce memory usage. Reducing the size of the raytraced image will also reduce memory usage, but of course your image will be smaller... Hope these suggestions help, Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you. --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057; dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] (no subject)
Hi Blanton You are probably looking for the symexp command. I don't remember the exact syntax, but there is a small help text. You can also try to search the mail archive. Best wishes Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net on behalf of Blanton Tolbert Sent: Sat 2006-03-04 15:01 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] (no subject) Hi pymol community I would like to recapitulate the crystal packing arrangement of a protein structure to look for neighbor interactions. Is it possible to do this in pymol? If so, please provide me some insight. Thanks, Blanton Tolbert Graduate Student University of Rochester Biophysics and Structural Biology 585-275-5189 blanton_tolb...@urmc.rochester.edu --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] NAMD/dcd
Hi Arturas!
A - relatively - easy way to read DCDs into PyMOL is:
* Convert the .dcd to .trr using catdcd 4.0
(http://www.ks.uiuc.edu/Development/MDTools/catdcd/). At the same time you can
concatenate multiple .dcd files, remove solvent, skip frames, etc.
* Convert the .trr file to a multi-model .pdb file using trjconv from the
Gromacs package (http://www.gromacs.org/) Here you can select eg. desired
residues (using make_ndx), skip frames, and align each frame to a reference
structure before writing the pdb file.
Using two programs may seem a bit complicated, but most likely you want to
concatenate files, remove solvent or do other processing anyway, so I think it
is ok :-)
This works quite nicely for me. If you want to look at every single frame of a
long MD with many atoms, you may run into problems with very large pdb files,
though.
Having the trajectory as a .trr file also gives the possibility of using
Gromacs' analysis tools, such as g_rms or g_rmsf.
There are some examples below...
Cheers,
Esben
-
# the structure is in system.pdb, system.psf and trajectories in
-0100.dcd ... 0900-1000.dcd.
# creating the stripped pdb file (removing solvent (residues called TIP3)):
grep -v TIP ../system.pdb solute.pdb
# creating the index file for catdcd (for removing solvent):
awk '/ATOM/ {print $2-1}' solute.pdb solute.idx
# making the stripped file in gromacs format.
/z/linux/catdcd4/LINUX/bin/catdcd4.0/catdcd -o wt_strip.trr -otype trr -i
solut.idx ../-0100.dcd ../0100-0200.dcd ../0200-0300.dcd ../0300-0400.dcd
../0400-0500.dcd ../0500-0600.dcd ../0600-0700.dcd ../0700-0800.dcd
../0800-0900.dcd ./0900-1000.dcd
--
# The per-residue rms and pdb file for putty cartoon
g_rmsf -f wt_strip.trr -s solute.pdb -oq test.pdb
# select group 4 for backbone
# load test.pdb in PyMOL and show it as putty cartoon:
pymol load test.pdb
pymol cartoon putty, test
pymol show cartoon, test
pymol hide lines, test
# The overall rmsd as a function of time
g_rms -f wt_strip.trr -s solute.pdb
# selecet group 0, compare to 1, and select group 0 again
# The resulting rmsd.xvg can be shown directly with xmgrace
(http://plasma-gate.weizmann.ac.il/Grace/):
xmgrace rmsd.xvg
-
#Showing MD ensemble of specific residues (here 100,101,102,103,200,201):
# run make_ndx
make_ndx -f solute.pdb -o site.ndx
# make a new group
r 100 101 102 103 200 201
# delete the other groups:
keep 14
# call it site
name 0 site
# save and quit:
q
# run trjconv to get a pdb file with every 100th frame for the site residues:
trjconv -f wt_strip.trr -o site.pdb -s solute.pdb -n site.ndx -fit
rot+trans-skip 100
# load site.pdb and solute.pdb in pymol
pymol load site.pdb
pymol load solute.pdb
# use a similar selection in pymol to align it to the reference structure:
pymol select solute and resi 100+101+102+103+200+201
pymol align siteCA, seleCA
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net on behalf of Warren DeLano
Sent: Fri 2006-02-10 20:08
To: ziemy...@osu.edu; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] NAMD/dcd
Arturas,
DCD suppot? Not yet -- we need someone to either donate, develop, or
fund code to support this key MD trajectory format.
Cheers,
warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
zie...@ecr6.ohio-state.edu
Sent: Friday, February 10, 2006 10:59 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] NAMD/dcd
HI !
I new one with PyMol and found it very promising for my
works. However, I need analyze MD trajectories DCD from NAMD.
Is there any clue to load DCD's, as manual talks only abaout
Amber format ?
Best
Arturas Z.
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RE: [PyMOL] movie of diffusion of atoms/molecules
Hi Satya You can use the command translate to move the individual objects in pymol. Is takes a list of 3 floating points numbers as the translational vector. I don't know how Pymol would handle 4000 objects, but an alternative might be to load them as states within one object, and then use the show all states command from the Movie menu. The translate command can also move the individual states independently. (If you also need to rotate the molecules, it gets more difficult :-) Another suggestion: If you have 4000 proteins, you may not need a very high level of detail for each molecule. You could save a lot by loading only the alpha carbon atoms and then increase their vdw-size to make them stick together: pymol alter my_object, vdw=3.0 pymol show spheres, my_object pymol sort Cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net on behalf of Satya Arjunan Sent: Sat 2006-02-11 03:56 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] movie of diffusion of atoms/molecules Hi all, I would like to use Pymol to visualize 3D simulation of lattice-based diffusion of molecules. The simulator provides the 3D coordinates (or the translational direction since they have fixed diffusion distance) of the molecules at everytime step. At the end of the simulation, I would like to feed the coordinates (or the translational direction) to Pymol using a python script and make a movie of this. What is a good way of implementing this with Pymol with lowest computational cost because there are about 4000 protein molecules altogether? I have come across a sample script at http://www.rubor.de/bioinf/tips_python.html#chempy which I think I can use to place the atoms/molecules in pymol. I am wondering if there is any other cost effective way of implementing this? Is it possible just to provide the translational angle and distance for certain molecules already in the model? Thanks in advance. satya --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Super-smooth surfaces
Hi Stephen
I also use smooth surfaces - for visualizing results from small angle
xray scattering, which is a low resolution technique. I use:
set solvent_radius, 4
alter my_protein, vdw=4
sort
show surface, my_protein
Maybe you can set solvent_radius a little bit higher, but not much, as
you will get holes in the surface like you see. You can adjust the
blobbiness by changing the vdw size.
Cheers
Esben
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Stephen Graham
Sent: 11. januar 2006 23:22
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Super-smooth surfaces
Hi there,
I am making a figure in which I would like an extremely
smooth molecular surface (I just want the protein as a blob
with little to no definition of surface features).
I tried setting the probe radius to a larger value:
set solvent_radius, 8
but this gives rise to ugly artefacts on the surface
('triangles' of surface seem to be missing). There seems to
be a whole raft of different settings for fine-tuning
surfaces (surface_carve_*, surface_trim_*, etc) but I am
afraid I do not know what they do and have been unable to
find documentation on them.
How can I make a surface happy (fully connected) after having
set the probe radius way up?
Thanks,
Stephen
--
Stephen Graham
Crystallography Group
School of Molecular and Microbial Biosciences
University of Sydney
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RE: [PyMOL] Geowall Testing
I'll try it when I get back to work tomorrow - but I'm a bit confused :-) The features you mention, haven't they been part of PyMOL for some time already? We have active stereo glasses for our workstations, and use the same PyMOL version (0.99beta14) for those and the Geowall. Cheers, Esben -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Mon 2005-10-17 22:06 To: EPF (Esben Peter Friis) Subject: RE: [PyMOL] Geowall Testing Esben, Great! Added: support for the internal gui, pop-up menus, sequence viewer, and command line when using a passive stereo setup (versus active stereo setups that cost about 10X more). Can you try the build at http://delsci.com/beta? Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com From: EPF (Esben Peter Friis) [mailto:e...@novozymes.com] Sent: Monday, October 17, 2005 12:58 PM To: Warren DeLano Subject: RE: [PyMOL] Geowall Testing Yep - we have one, which we use mostly for PyMOL presentations :-) Stereo already works great, so I'm curious what you have in mind. The computer connected to it is running Linux (Fedora Core 2) and uses an Nvidia Quadro 750GLX card. Cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net on behalf of Warren DeLano Sent: Mon 2005-10-17 16:27 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Geowall Testing PyMOL Users: Regarding geowalls [also known as dual-projector passive stereo setups that use polarized lenses glasses to deliver low-cost stereo 3D to large audiences]... Does anyone have one set up right now who might be able to test a new PyMOL build with improved geowall stereo support? Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com --- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Geowall Testing
Ah... That make things a bit clearer :-) We do have a geowall, but the Linux driver supplied by Nvidia directly supports sending the left and right images of the quad-buffered stereo to the two separate video heads on the card, which are then connected to the two projectors. This eliminates the need for the very expensive active-to-passive stereo converter. This do require a Quadro-card, though. It is not supported by the cheaper GeForce cards. I think the Linux driver also support the type of stereo you mention here: Making a kind of side-by-side stereo, which is then converted to real stereo by doubling the desktop width, and splitting desktop between the two heads. I haven't tried, but I guess that is also supported by the GeForce cards. If it is not too difficult, I'll give it a try! I would argue that even though you can save a few hundred bucks (difference between a Quadro and a GeForce card), the Quadro card solution is easier. A Quadro FX 1300 card is around for about $300-400, which is still small compared to the Geowall system. But for Mac (and maybe Windows?) users, this driver option may not be available. Cheers Esben -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Mon 2005-10-17 22:43 To: EPF (Esben Peter Friis) Subject: RE: [PyMOL] Geowall Testing Esben, If that is the case, then you don't actually have a Geowall -- you have a professional stereo device setup that converts the active-stereo signal sent from the nVidia cards into a passive-stereo signal for the two projectors. That's equivalent to QBS stereo on a CRT with glasses, but typically costs quite a bit more (as much as $50k USD) Geowalls are a low-end alternative the geologists came up with a few years back. Instead of requiring a stereo-capable video card, they use a normal (not necessarily stereo-capable) dual-headed video card to drive two projecters straight from the PC. That can bring the cost down to under $5k total, but it means that the software needs to draw the complete image twice, including the GUI, hence these changes. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of EPF (Esben Peter Friis) Sent: Monday, October 17, 2005 1:30 PM To: Warren DeLano Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Geowall Testing I'll try it when I get back to work tomorrow - but I'm a bit confused :-) The features you mention, haven't they been part of PyMOL for some time already? We have active stereo glasses for our workstations, and use the same PyMOL version (0.99beta14) for those and the Geowall. Cheers, Esben -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Mon 2005-10-17 22:06 To: EPF (Esben Peter Friis) Subject: RE: [PyMOL] Geowall Testing Esben, Great! Added: support for the internal gui, pop-up menus, sequence viewer, and command line when using a passive stereo setup (versus active stereo setups that cost about 10X more). Can you try the build at http://delsci.com/beta? Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com From: EPF (Esben Peter Friis) [mailto:e...@novozymes.com] Sent: Monday, October 17, 2005 12:58 PM To: Warren DeLano Subject: RE: [PyMOL] Geowall Testing Yep - we have one, which we use mostly for PyMOL presentations :-) Stereo already works great, so I'm curious what you have in mind. The computer connected to it is running Linux (Fedora Core 2) and uses an Nvidia Quadro 750GLX card. Cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net on behalf of Warren DeLano Sent: Mon 2005-10-17 16:27 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Geowall Testing PyMOL Users: Regarding geowalls [also known as dual-projector passive stereo setups that use polarized lenses glasses to deliver low-cost stereo 3D to large audiences]... Does anyone have one set up right now who might be able to test a new PyMOL build with improved geowall
RE: [PyMOL] Implementing PCA
Hi Yusuf The OpenSource statistics software R (http://www.r-project.org) has many packages that can do PCA, PLS and other multivariate analyses, which we have used with great success. There are several Pyhton interfaces to R, eg. http://www.omegahat.org/RSPython/ http://rpy.sourceforge.net/ I must admit I haven't tried these, but it appears to be a shortcut to do advanced statistics within PyMOL Cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net on behalf of Warren DeLano Sent: Tue 2005-07-19 18:17 To: tanri...@stud.uni-frankfurt.de; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Implementing PCA Yusuf, You can use the Numeric Python or Numarray modules to perform such tasks. The windows builds include a (somewhat dated) version of Numeric by default that can be accessed as follows: from Numeric import * http://numeric.scipy.org/ Numeric's Linear algebra docs http://numeric.scipy.org/numpydoc/numpy-18.html#pgfId-303015 Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of tanri...@stud.uni-frankfurt.de Sent: Tuesday, July 19, 2005 6:08 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Implementing PCA Hi everybody, I want to write a PCA script (.py) for use within PyMOL. Are there any matrix operations or eigenvector calculations implemented by now, or do I have to integrate other libraries? How do I do that in Linux? Thanks for your help. Yusuf -- Yusuf Tanrikulu Bioinformatics Diploma Student Department of Biosciences Johann Wolfgang Goethe-University Marie-Curie-Str. 11 D-60439 Frankfurt, Germany Email: tanrik...@bioinformatik.uni-frankfurt.de --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477alloc_id=16492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77alloc_id492op=ick ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] multi cpu rendering
Hi Neil Have you tried the command set max_threads, 4 That should enforce 4 threads, even on single CPU machines. Then it's up to the kernel scheduler to distribute them to the defferent CPUs Cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Neil Ranson Sent: 19. april 2005 13:34 To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] multi cpu rendering Dear All, I've been preparing figures for a manuscript on a Sun v40z with 4 x Opteron 850 cpu's and 8Gb of memory (and Suse9.0). When I start pymol: pymol.com -c script.pml pymol says that it detects 4cpu and enables multithreaded rendering, but I never see it using more than one cpu. Especially for producing ray traced movies, I'd really like to see the multiprocessing benefits. Does anyone have any suggestions? Cheers, Neil
RE: [PyMOL] high end graphics
Is it possible to get graphics output higher than 72 dpi? Yes: - The OpenGL rendered graphics can only be saved in the resolution displayed on the screen (using the png command) - The raytracer can generate pictures of any size, eg. ray 8000, 6000; png mypic.png would generate the picture in 8000x6000 pixels and save it as mypic.png. If you turn off shadows, you will get a picture which is very close to the OpenGL rendered one. You can check by just using the ray command, which generates the raytraced image in the window. cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Joel Tyndall Sent: 11. november 2004 01:17 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] high end graphics Hi folks, Is it possible to get graphics output higher than 72 dpi? Cheers Joel -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 --- This SF.Net email is sponsored by: Sybase ASE Linux Express Edition - download now for FREE LinuxWorld Reader's Choice Award Winner for best database on Linux. http://ads.osdn.com/?ad_id=5588alloc_id=12065op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/p ymol-users
RE: [PyMOL] stereo projection with PyMOL
Hi Joe [cut - two projector stereo projetion system ] What kind of uses does your system see? Is it predominately used by researchers, or by classes, or a good mix between the two? A very rough estimate - 60% internal work, discussions with wet chemists, molecular biologists and patent guys. - 20% presentations for costumers and external collaborators - 20% presentations for students (university, a few from high school) The show-off effect is still good, as this kind of systems are not yet very common. But it is very valuable also for real work, as it is much easier to see than the 21 screen + shutter glasses, particularly if we are more than two people. BTW - apart from PyMOL, the system also runs VMD and InsightII (Accelrys) in stereo. There are some pictures of the system here: http://62.79.21.192.adsl.vby.tiscali.dk/~epf/projection/ Cheers, Esben
RE: [PyMOL] electrostatic
Are you using the same platform for both Grasp and Pymol? I don't think that big-endian maps (written by an SGI computer) can be read by a little-endian platform, such as a x86 based PC. - Esben The problem is getting the phi map in grasp. Can somebody explain me how to do it? This is what we did and worked (we now using Delphi), try it. -- *On the SGI computers: 1) Start up the computer, log in and in a command line prompt, change the directory to where the .pdb fi le, .siz file and .crg files are located. 2) Run grasp (command: /hhmi/software/grasp/grasp) 3) Open up the menu by right-clicking on the window 4) With the menu open, right-click on the Read option. 5) Right-click on the PDB File option and load the .pdb file. 6) Open the read menu again (steps 3-4), and select the Radius/Charge File option, then load the raidus file. Repeat again, loading the charge file. 7) Open the main menu, click on display, show, molecular surface. 8) Open the main menu, click on calculate, new potential map. 9) Open the main menu, click on calculate, Pot. via map at surface/atoms 10) Open the main menu, click on write, potential map, internal map, let me enter it. In the command lin e prompt, type in the name of the file (namefile.phi) === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone:(410)455-6347 (primary) (410)455-2718 (secondary) fax: (410)455-1174 email:c...@hhmi.umbc.edu === --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562alloc_id=6184op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Ball Stick representation
I have mad a lot of these pictures, and the solution is to create two objects for the substrate. object1, displayed as sticks in the desired color, and object2 dipslayed as spheres in the desired color(s) and then set sphere_scale, 0.3, object2 Example (if the file contains a residue named NAD) load molecule.pdb, complex create prot, complex and not resn NAD create nad1, complex and resn NAD create nad2, nad1 disable complex show sticks, nad1 color grey70, nad1 show spheres, nad2 set sphere_scale, 0.3, nad2 Hope this helps Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Zach Sent: 18. maj 2004 23:36 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Ball Stick representation Hello to all, I have a protein that contains a substrate and for which I want to create a picture. For the substrate I would like to use a ball and stick representation such that the spheres are colored by atom type and the sticks are on a single color. My problem is that I have not been able to give different color schemes to the sticks and spheres. How do I do that? Any help is greatly appreciated. Thanks, Zach --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562alloc_id=6184op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Updated OpenGL Hardware Recommendations
Hi Peter I'm very happy with the cheap gamers glasses. They are light, much lighter than the old CrystalEyes we have for our SGI-systems, and also more reliable (ie. when they dont work, they just need new batteries :-) The batteries (CR2016) have less capacity than the ones in CrystalEyes (CR2032) but thats a minor issue. Note that these glasses only work with Linux if the graphics card has a VESA stereo connector (like the Quadro cards). I also tried some wired glasses (Eye3D 4in1), which were also good, but they needed a VGA passthrough cable, which disturbs the signal a bit, resulting in a slightly blur image on the screen. The advantages are no batteries, and they don't need a VESA stereo connector on the graphics board. We have succesfully run stereo under Linux with Xig X-server and a ATI 9000pro card - and XF86/Nvidia driver/Nvidia GeForce4 card. However, I'm not sure these glasses are available anymore. Best regards Esben -Original Message- From: Peter Haebel [mailto:peter.hae...@staff.uni-marburg.de] Sent: 12. maj 2004 10:05 To: EPF (Esben Peter Friis) Subject: Re: [PyMOL] Updated OpenGL Hardware Recommendations Hi Esben, thanks for your response. we just bought an Nvidia Quadro4 380GLX and everything runs fast and fine :) i am quite interested in your stereo glasses. are you happy with quality and durability? we are currently thinking about Nuvision glases which cost about $500 (here in germany). cheers peter On Wednesday 12 May 2004 08:50, you wrote: Hi Peter Your posting is a few weeks old, but I could see no replies yet, so I'll try :-) We have single-CPU Dell machines (3 GHz, 2GB RAM), but I suppose you just buy CPU, disk and memory according to your needs (and money :-) You don't write anything about OS, but according to your ps line, I assume it is Linux. We use Nvidia Quadro FX3000 graphics, which I can recommend. It is really fast (compared to our old SGIs), and the setup is straightforward. Just download the driver from nvidia.com, run the installer, and add a few things in the XF86Config file (see Nvidia readme file). We have successfully tested the driver (including stereo support) with Pymol on the following OSes: RH 9.0 Fedora Core 1 Enterprise WS 3 Windows XP I have no experience with O, but Pymol, VMD and Accelrys insightII graphics works fine i stereo. We use glasses from http://www.edimensional.com/, which are about $100 for emitter and glasses, and $50 for extra glasses w/o emitter. There is also a breakout box for use with cheaper graphics cards, but if you use the FX3000 (or any other Quadro card), you just throw away the breakout box and connect the emitter directly to the VESA stereo connector on the graphics card. We also have a 3D projection system with two projectors and polarization filters. The Quadro cards are dual head, and the Nvidia driver is capable of sending the L/R stereo images to different displays (requires additional setup in XF86Config, again - see the readme file). So no problems here either. (I haven't been able to make this work under Windows yet :-) Cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Peter Haebel Sent: 27. april 2004 10:00 To: war...@delanoscientific.com; al...@xray.bmc.uu.se Cc: pymol-users@lists.sourceforge.net; o-i...@o-info.imsb.au.dk Subject: [PyMOL] Updated OpenGL Hardware Recommendations Dear all, we just considering to purchase new linux pcs and i would be very interested in the latest hardware recommendations? we are planning to use these machines for stereo visualization with pymol and O. cheers, peter ps. has the pymol Xig Summit2.2 problem been resolved? -- ___ Dr. Peter Haebel Philipps-Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 D-35032 Marburg phone: +49-6421-28-25072 fax: +49-6421-28-28994 email: peter.hae...@staff.uni-marburg.de http://www.agklebe.de --- This SF.Net email is sponsored by: Oracle 10g Get certified on the hottest thing ever to hit the market... Oracle 10g. Take an Oracle 10g class now, and we'll give you the exam FREE. http://ads.osdn.com/?ad_id149alloc_id66op=ick ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/p ymol-users -- ___ Dr. Peter Haebel Philipps-Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 D-35032 Marburg phone: +49-6421-28-25072 fax: +49
RE: [PyMOL] Updated OpenGL Hardware Recommendations
Hi Peter Your posting is a few weeks old, but I could see no replies yet, so I'll try :-) We have single-CPU Dell machines (3 GHz, 2GB RAM), but I suppose you just buy CPU, disk and memory according to your needs (and money :-) You don't write anything about OS, but according to your ps line, I assume it is Linux. We use Nvidia Quadro FX3000 graphics, which I can recommend. It is really fast (compared to our old SGIs), and the setup is straightforward. Just download the driver from nvidia.com, run the installer, and add a few things in the XF86Config file (see Nvidia readme file). We have successfully tested the driver (including stereo support) with Pymol on the following OSes: RH 9.0 Fedora Core 1 Enterprise WS 3 Windows XP I have no experience with O, but Pymol, VMD and Accelrys insightII graphics works fine i stereo. We use glasses from http://www.edimensional.com/, which are about $100 for emitter and glasses, and $50 for extra glasses w/o emitter. There is also a breakout box for use with cheaper graphics cards, but if you use the FX3000 (or any other Quadro card), you just throw away the breakout box and connect the emitter directly to the VESA stereo connector on the graphics card. We also have a 3D projection system with two projectors and polarization filters. The Quadro cards are dual head, and the Nvidia driver is capable of sending the L/R stereo images to different displays (requires additional setup in XF86Config, again - see the readme file). So no problems here either. (I haven't been able to make this work under Windows yet :-) Cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Peter Haebel Sent: 27. april 2004 10:00 To: war...@delanoscientific.com; al...@xray.bmc.uu.se Cc: pymol-users@lists.sourceforge.net; o-i...@o-info.imsb.au.dk Subject: [PyMOL] Updated OpenGL Hardware Recommendations Dear all, we just considering to purchase new linux pcs and i would be very interested in the latest hardware recommendations? we are planning to use these machines for stereo visualization with pymol and O. cheers, peter ps. has the pymol Xig Summit2.2 problem been resolved? -- ___ Dr. Peter Haebel Philipps-Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 D-35032 Marburg phone: +49-6421-28-25072 fax: +49-6421-28-28994 email: peter.hae...@staff.uni-marburg.de http://www.agklebe.de --- This SF.Net email is sponsored by: Oracle 10g Get certified on the hottest thing ever to hit the market... Oracle 10g. Take an Oracle 10g class now, and we'll give you the exam FREE. http://ads.osdn.com/?ad_id149alloc_id66op=ick ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/p ymol-users
RE: [PyMOL] Updated OpenGL Hardware Recommendations
Whops, sorry You _do_ write it is Linux PCs ;-) - Esben
[PyMOL] Rotation of maps when aligning
Hi PyMOLers I have a bunch of structures, for which I have calculated electrostatic potential maps (using Gromacs and MEAD). I can easily load the structures and corresponding maps into PyMOL and display a color coded surface. But when I try to align the structures, only the atomic coordinates are transformed - the electrostatic maps remain in their original orientations. As PyMOL update the surfaces after the alignment, the resulting surface colors are completely wrong. Doing things in another order doesn't help. As far as I can see from a posting from March 3rd (by John Eksterowicz), the problem is exactly the same for a density map. In my case, the workaround is to align all the structures before I do the electrostatic calculation - but it would be better if the maps could be assigned to the coordinate system of a structure. In this way, the maps would still be vaild after a 3D-alignment. Is there a way to do this? Best regards Esben
RE: [PyMOL] Question
Hi Avram This is possible in cartoon mode in the newer versions of PyMOL (i don't remember exactly from which). You have to select highlight color in the cartoon menu. The default color is grey, but can be changed by set cartoon_highlight_color, color_name, object_name Cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net To: pymol-users@lists.sourceforge.net Sent: 19-12-03 20:37 Subject: [PyMOL] Question Hi, does anyone know how to color the inside of helices a different color than the outsides? thanks Avram -- Avram M. Slovic Biochemistry and Molecular Biophysics University of Pennsylvania 420 Curie Blvd. 1010 Stellar Chance Bldg. Philadelphia, PA 19104 L:215-898-3496 --- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278alloc_id=3371op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Electrostatic potential maps in PyMOL
Hi Paulo, Andreas - and other PyMOLers doing electrostatics Sorry for the late reply - Our department is being relocated, and I've spent most of my time on that lately There was a problem with the posting, where some of the source code lines were wrapped. In most cases this was no problem, but in one line it is fatal: fprintf(outfile,Map converted from MEAD AVS (fld) file ); The string in this line must be exactly 60 (sixty) characters long - there should be 22 spaces in the end. But I will strongly recommend that you use version 0.91 of PyMOL instead, as this reads the .fld maps from MEAD directly without the need for conversion. Furthermore, it reads maps of any size, not just 65x65x65. v0.91 is still only available from CVS, but maybe we can convince Warren to make an official release soon :-) Best regards Esben -Original Message- From: Paulo Martel To: EPF (Esben Peter Friis) Sent: 14-09-03 20:28 Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL Dear Esben, no matter how hard I try, I cannot make pymol read a phi map converted from avs with your utility. The .fld file was generated with the potential program in the latest MEAD distribution and converted with problems to .phi (the values output by fld2phi seem normal). When I try to load the grid into pymol, it displays and absurdly big range like it was read the numbers in the wrong endianess. I am using pymol 0.90 on a RedHat 7.3 PIV Linux system, and compiled your program with gcc. Best regards, Paulo On Wed, 2003-07-09 at 15:48, EPF (Esben Peter Friis) wrote: Hi PyMOL users, MEAD's potential maps can be used in PyMOL, but it requires a little more than a bit of tweaking, as the maps are in the AVS .fld format, which can not be read by PyMOL. (These maps can be read by Dino, as Paulo just mentioned). Also, PyMOL reads (as far as I can see) only big-endian phi-maps. I have written a small program, which does the conversion from .fld to big-endian-.phi, so the maps can be read by PyMOL. It just finished it today, and it has only been tested on Linux (i386), so beware ;-) To create a nice electrostatic surface, you need: * Gromacs (not strictly necessary, but makes life easier) Download from http://www.gromacs.org * MEAD. Download from http://www.scripps.edu/bashford/ * fld2phi, source code quoted below (sorry, but I don't have access to our external web server, and it's only about 4kb). * PyMOL, of course (v0.88 or newer). Here is an example how to create everything from scratch for 4PTI.pdb Gromacs steps - 1) use pdb2gmx to create .gro and .top files: pdb2gmx -f 4PTI.pdb -o 4PTI.gro -p 4PTI.top 2) use grompp to create .tpr file: grompp -f 4PTI.mdp -p 4PTI.top -o 4PTI.tpr -c 4PTI.gro The file 4PTI.mdp contains the parameters for the Gromacs simulation. But as we are not going to do any simulation this time, an empty file is ok. It can be created with touch 4PTI.mdp. 3) use editconf to create a MEAD-readable pdb file: editconf -f 4PTI.tpr -mead -o 4PTI.pqr.pdb The output pdb file must then be renamed to be recognized by MEAD: mv 4PTI.pqr.pdb 4PTI.pqr MEAD steps -- 1) create a .ogm file which specifies the grid size. Notice that PyMOL can only handle grids which are 65x65x65 points, so your only option is to change the spacing between points. You can specify focussing options in the .ogm file, but only the coarsest grid is written anyway, so you only need one line in the 4PTI.ogm file: ON_GEOM_CENT 65 1.0 See documentation for other centering options (first parameter). Next number is the number of grid points on each side (must be 65 to be readable by PyMOL). The last number is a real specifying the distance between grid points. 2) Run 'potential' to create the grid: potential -epsin 2 -CoarseFieldOut 4PTI 4PTI The epsin option is mandatory and specifies the internal (in the protein) dielectric constant. The program will say something like: WARINING from potential main program: Could not open field point file, 4PTI.fpt, for reading. Exiting without giving any potentials. This can be ignored. The program still writes out a 4PTI.fld file with the grid. Notice that this file in not overwritten, so you must delete it manually if it already exists. Convert to PyMOL readable grid -- 1) Use the fld2phi to convert the .fld file to a big-endian .phi grid file: fld2phi 4PTI.fld 4PTI.phi This sould create a 4PTI.phi file which is readable by PyMOL. PyMOL steps --- 1) Load the structure including the hydrogens built by Gromacs: load 4PTI.pqr, 4PTI 2) Create a selection of the water: select water, 4PTI and resn SOL 3) Remove the water atoms: remove water 4) Show the surface of the 4PTI object: show surface, 4PTI 5) Load the electrostatic grid: load 4PTI.phi, map You can show the extent of the grid box by clicking
RE: [PyMOL] Nuvision stereo glasses?
No, actually I didn't, I thought is was enabled by default, so I must admit I overlooked it in the driver instructions. I have to add the line Option Stereo 1 to the XF86Config file. That's a pity - the FX1000 is probably faster than the 750XGL :-) Well - the supplier accidentially swapped my and another costumer's orders - so I was honest and sent it back :-) Also, even with the cheap GeForce 4MX card currently in the machine, the (mono) graphic performance is incredible - I guess it's an order of magnitude faster than the VPro6 graphics on our SGIs :-) Cheers, Esben -Original Message- From: Warren L. DeLano To: EPF (Esben Peter Friis) Sent: 21-07-03 18:19 Subject: RE: [PyMOL] Nuvision stereo glasses? Esben, Are you sure you correctly configured the nVidia driver (XF86Config) for Stereo? It's not automatic, but as AFAIK, all the FX's are QBS capable. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of EPF (Esben Peter Friis) Sent: Sunday, July 20, 2003 11:39 PM To: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Nuvision stereo glasses? Hi all! My personal bias is that the added cost to obtain real QBS hardware with built-in stereo support is well worth the money in terms of time saved on bugs and hassles such as this. Yes! Real quad-buffered stereo is IMHO crucial for molecular modelling work ;-) Under Linux, the nVidia Quadro4 750XGL does a fine job, has a three-pin stereo sync plug, and works with the Nuvision glasses and emitters. While I haven't tested the higher-end FX series, I have every reason to believe that they would also work just fine given nVidia's unified driver architecture. I doesn't work for me :-( I ordered a Quadro4 750XGL, and the vendor sent me a Quadro FX1000 by mistake. I didn't notice at first, and just installed the card. Works fine and very fast with the 1.0-4363 version of the Linux driver - but neither PyMOL or VMD detects any hardware stereo I have to get it replaced by a 750XGL or 900XGL. We have some older stereographics glasses, which I expect will work with the Nvidia cards. But we have also bought a set of Eye3D premium glasses. They come with a VGA pass-through cable, which can catch the sync signal from any VGA output. They also support different stereo modes, including interlacing, page-flipping, sync-doubling, and line-blanking. You get two sets of glasses (one wired, one IR) for €179 or $199. This works nice with PyMOL and the Xig X-server on an ATI Radeon 9000 card, and the Scanline interleave (interlaced) stereo mode in VMD works fine with these glasses and any graphics adapter. Maybe scanline interleave could be a stereo option in PyMOL - it is definitely inferior to quad-buffered stereo, but it works with _any_ graphics card and doesn't require a special driver. (I would still go for QBS, though :-) Cheers Esben --- This SF.net email is sponsored by: VM Ware With VMware you can run multiple operating systems on a single machine. WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the same time. Free trial click here: http://www.vmware.com/wl/offer/345/0 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Electrostatic potential maps in PyMOL
Hi PyMOL users, MEAD's potential maps can be used in PyMOL, but it requires a little more than a bit of tweaking, as the maps are in the AVS .fld format, which can not be read by PyMOL. (These maps can be read by Dino, as Paulo just mentioned). Also, PyMOL reads (as far as I can see) only big-endian phi-maps. I have written a small program, which does the conversion from .fld to big-endian-.phi, so the maps can be read by PyMOL. It just finished it today, and it has only been tested on Linux (i386), so beware ;-) To create a nice electrostatic surface, you need: * Gromacs (not strictly necessary, but makes life easier) Download from http://www.gromacs.org * MEAD. Download from http://www.scripps.edu/bashford/ * fld2phi, source code quoted below (sorry, but I don't have access to our external web server, and it's only about 4kb). * PyMOL, of course (v0.88 or newer). Here is an example how to create everything from scratch for 4PTI.pdb Gromacs steps - 1) use pdb2gmx to create .gro and .top files: pdb2gmx -f 4PTI.pdb -o 4PTI.gro -p 4PTI.top 2) use grompp to create .tpr file: grompp -f 4PTI.mdp -p 4PTI.top -o 4PTI.tpr -c 4PTI.gro The file 4PTI.mdp contains the parameters for the Gromacs simulation. But as we are not going to do any simulation this time, an empty file is ok. It can be created with touch 4PTI.mdp. 3) use editconf to create a MEAD-readable pdb file: editconf -f 4PTI.tpr -mead -o 4PTI.pqr.pdb The output pdb file must then be renamed to be recognized by MEAD: mv 4PTI.pqr.pdb 4PTI.pqr MEAD steps -- 1) create a .ogm file which specifies the grid size. Notice that PyMOL can only handle grids which are 65x65x65 points, so your only option is to change the spacing between points. You can specify focussing options in the .ogm file, but only the coarsest grid is written anyway, so you only need one line in the 4PTI.ogm file: ON_GEOM_CENT 65 1.0 See documentation for other centering options (first parameter). Next number is the number of grid points on each side (must be 65 to be readable by PyMOL). The last number is a real specifying the distance between grid points. 2) Run 'potential' to create the grid: potential -epsin 2 -CoarseFieldOut 4PTI 4PTI The epsin option is mandatory and specifies the internal (in the protein) dielectric constant. The program will say something like: WARINING from potential main program: Could not open field point file, 4PTI.fpt, for reading. Exiting without giving any potentials. This can be ignored. The program still writes out a 4PTI.fld file with the grid. Notice that this file in not overwritten, so you must delete it manually if it already exists. Convert to PyMOL readable grid -- 1) Use the fld2phi to convert the .fld file to a big-endian .phi grid file: fld2phi 4PTI.fld 4PTI.phi This sould create a 4PTI.phi file which is readable by PyMOL. PyMOL steps --- 1) Load the structure including the hydrogens built by Gromacs: load 4PTI.pqr, 4PTI 2) Create a selection of the water: select water, 4PTI and resn SOL 3) Remove the water atoms: remove water 4) Show the surface of the 4PTI object: show surface, 4PTI 5) Load the electrostatic grid: load 4PTI.phi, map You can show the extent of the grid box by clicking on the object called map in the object list to the right. 6) Create a color ramp object: ramp_new e_lvl, map, [-0.02,0.00,0.02] 7) Color the surface according to the grid and map: set surface_color, e_lvl, 4PTI Thats it. You can change the color scale on the fly by issuing another ramp_new command with other numbers. The 3 numbers are red-point, white-point and blue-point, respectively. The scale can also be changed by ctrl+mid-click while you drag the color scale. It is also possible to create one or more contour surfaces: isosurface contour1, map, -0.05 where contour1 is the object name of the surface (choose whatever you want), map is the object name of the electrostatic potential map and the number is the contour level. The commands isomesh and isodot have the same syntax and do exactly what you think. Best regards (and please forgive me for quoting source code here :) Esben ** * Source code for fld2phi * * save as: fld2phi.c* * compile with: gcc -o fld2phi fld2phi.c* ** /* This is fld2phi.c */ /* This program reads little-endian AVS fields (.fld-files) from MEAD and */ /* convert it to big-endian .phi maps readable by PyMOL */ /* Tested on i386-Linux only */ /* (c) Esben Friis, 2003 */ /* INCLUDES --- */ #include stdio.h #include stdlib.h /* - DEFINES --- */ #define VERSION 1.0 #define DATE2003-07-09 /* - FUNCTIONS - */ int get_fld_header (char
