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Pymol For Windows 10

64-bit Windows 10 or newer 64-bit macOS 10.12+, including Apple Silicon (M1) with Rosetta 2 64-bit Linux, including CentOS 7+, Ubuntu 18.04+, and others (glibc 2.12+). Unable to run PyMol on Windows 10 - build from source #60. Eusebiu opened this issue Oct 29, 2019 6 comments Labels. Copy link Quote reply.
MAC Install
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Pymol Free Download
See Full List On Pymolwiki.org

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.

Let's figure out together what stereo solutions work well in this brave new post-CRT world! Acer 7741g drivers.
2Active Stereo 3D (High-Refresh) Displays2.1LCD Displays (120 Hz)2.1.1NVidia NVision 3D Setup2.1.1.3Installation Instructions
3Passive Stereo 3D Displays3.1One Piece Multi-layer LCD Displays3.1.2LG
5Stereo 3D Projectors
CategoriesActive Stereo 3D -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
Passive Stereo 3D -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
Autostereoscopic 3D -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.
Active Stereo 3D (High-Refresh) DisplaysThis solution would be analogous to using desktop CRT monitors with shutter glasses. 
LCD Displays (120 Hz)ACER GD235HZ. 1920x1080 120Hz 2ms .
Planar SA2311W. This is a high-end 23' 3D-ready monitor. The resolution is 1900x1280 and has a 2ms refresh time. This worked well for us.
ViewSonic VX2265wm (VX2268wm in Europe) - On the market and verified working under FC 12
Samsung 2233RZ - On the market. Quad buffered stereo in Linux works with a G8x based graphics core or better Quadro FX card with the 3 pin mini din stereo connector (currently, the cheapest card that works in Linux is the Quadro FX 3700), 195.22 (or newer) nvidia linux binary driver, and the Nvidia 3d vision kit. Even though the Quadro FX 1400/3450/4000 cards have a 3 pin stereo connector, these will not work with Nvidia 3D vision since these have core versions less than G8x. For more information see this forum post at the Nvidia Forums. - SP
USB only based stereo with the 3D vision kit works only in MS Windows (e.g. with a low end Quadro FX 370 that has no 3 pin mini din stereo connector). For more information see this forum post at the Nvidia Forums. - SP
The 195.22 Nvidia linux drivers do not support the Samsung 2233RZ in Stereo mode 3 or 10 for quad buffered stereo with other stereo kits, emitters, or goggles such as those purchased from NuVision, Stereographics, or Edimensional. You cannot use NuVision, Stereographics, or Edimensional goggles with the Nvidia 3D Vision emitters. - SP
NVidia 3D NVision kit only supports DirectX software for GeForce (gaming cards) on Windows; users are reporting that they are not able to run PyMOL with NVision with these cards. Get a newer model low end quadro (> G8x graphics core) without the 3 pin mini din (e.g. Quadro 370) or with the 3 pin mini din (e.g. Quadro 3700) for Windows.
NVidia NVision 3D SetupThe NVidia 3D NVision setup provides a very nice 3D experience. You need the following to enable PyMOL to show NVision 3D on Windows. Please review the hardware and software requirements before moving on to the installation and setup.
Necessary HardwareMonitor: 120 Hz LCD: a 2233RZ or a Fuhzion vx2265wm
Cable: Dual Link DVI cable; most 120Hz monitors will come with this cable--regardless, the cable is necessary
Quadro Card: recent Quadro series graphics card (not a GeForce card) such as an FX 380 or 570 or later. The GeForce cards do not support windowed openGL stereo, so we do not support these series of cards for the NVision 3D solution. For linux, you must have a quadro card that has a 3 pin mini din connector. The cheapest/oldest card that will work with linux is the Quadro 3700.WARNING: The Quadro FX1400 does not support 3d vision stereo on Windows7 or Linux.
Emitter: 3D Vision hardware kit (an emitter with 3D shutter glasses). For Linux, make sure your kit comes with the 3 pin mini din 'VESA' to 2.5mm stereo cable to connect from the stereo output on the video card into the emitter. See the 3 pin Mini-DIN connector article for tips on how to make one of these cables if yours is missing.
GeForce Cards from series 400 onward have gained OpenGl support in recent Nvidia driver iterations (314+). This allows Pymol to be viewed in 3D using the quad buffered stereo setting with a GeForce card, 120Hz screen and 3D Vision kit.
Necessary SoftwareWindows XP 32 bit (testing other OSs soon!), Windows Vista
Latest Quadro Drivers from NVidia.
Latest Graphics drivers for the NVision system--under Product Type choose 3D Vision.
Installation InstructionsSystem SetupInstall the Quadro Graphics Drivers and reboot your machines
Install the NVision Installation, hooking up the 3D emitter and glasses as directed in the instructionsMake sure the 3D demos work
Complete the 3D Vision Drivers install (I had errors/warnings about old drivers but this did't matter)
Specify how to drive the 3D by, click on
Windows Start Button > Control Panel > NVidia Control Panel > Manage 3D Settings (tab) > Global Settings (tab on the right) > Base Profile (tab). Then, under Settings choose Stereo - Display Mode. Next, select Generic Active Stereo (with NVidia IR Emitter). If you have a DLP monitor/TV choose the corresponding DLP option. You must also set Stereo - Enable to on.Running PyMOL

That's it! PyMOL should now work in Quad Buffered 3D Stereo using the NVidia 3D NVision system. To run PyMOL in 3D mode on:
Windows
Start > PyMOL > PyMOL > PyMOL 3D Launch (last menu option) > PyMOL Stereo (Quad Buffered 3D)Linux
pymol -S -t 1Note that hardware stereo may not work in Xorg unless window compositing is turned off; Gnome3, Unity, etc all use window compositing as part of their eye candy. A window manager that should work by default is the MATE desktop. Install this if you have troubleMac
MAC InstallSorry, at this time the NVision system is not known to work on Macs.DLP Projection TelevisionsProjection televisions tend to be too large and fuzzy for desktop use. Also, a band of about 20 pixels around on the edge of the display are invisible, and this limitation cannot be eliminated through overscan since the image must be scanned at native resolution in order to support stereo 3D. The workaround is to shrink the PyMOL window to cover the visible portion of the screen. It is worth noting that true 3D-capable LCDs (as distinct from 3D-capable HDTVs) do not suffer from this problem.
Aside from the above concerns, the quality of the DLP stereo 3D effect is exceptional: there is absolutely no ghosting or cross-talk between the two images. 
Samsung 3D-Ready DLP HDTVs - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD
Mitsubishi 3D-Ready DLP HDTVs - not yet tested, but are expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD
See The 3D HDTV List for more 3D-capable HDTV options.
Passive Stereo 3D DisplaysOne Piece Multi-layer LCD DisplaysAffordable!
ZalmaniZ3D, the original supplier of Zalman display drivers has ceased operation and support as of 31 July 2012. DO NOT PURCHASE THESE MONITORS WITHOUT FURTHER CONFIRMATION of display support, the iZ3D support (required drivers, etc) is not activatable. If you do have further information, please post it here.Jedgold 12:21, 12 September 2012 (CDT)
Zalman 22-inch 3D LCD monitor - works with PyMOL 1.2b3 & later without any special drivers. Great stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo mode, but even so, this 650 USD display provides excellent 3D molecular visualization in both full-screen in windowed modes. - WLD (The Zalman ZM-M220W is DeLano Scientific's RECOMMENDED SOLUTION as of Feb 11, 2009!).
Zalman 24-inch 3D LCD monitor - also works with PyMOL 1.2b3 & later under LINUX (Centos 5 x86_64 plain kernel + NVidia driver from ELRepo). I'm using an NVidia Quadro FX 580 (G96GL) graphics card (£125). Monitor cost around £350. PyMOL automagically detects that quad buffered stereo is available on startup.--Bosmith 16:32, 2 December 2010 (UTC)
LGLG DM2752D This (and other LG passive 3D monitors/TVs) work with PyMOL. I'm driving them using NVidia Quadro 600 graphics cards under LINUX (CentOSes 5, 6 & 7) with the NVidia driver from ELRepo.
On Linuxsetup by editing the xorg.conf file:
in the Device section of xorg.conf add:

This page is for aggregating the latest know-how and links to current Stereo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-hand experiences while using the displays for real work and teaching.
Let's figure out together what stereo solutions work well in this brave new post-CRT world! Acer 7741g drivers.
2Active Stereo 3D (High-Refresh) Displays2.1LCD Displays (120 Hz)2.1.1NVidia NVision 3D Setup2.1.1.3Installation Instructions
3Passive Stereo 3D Displays3.1One Piece Multi-layer LCD Displays3.1.2LG
5Stereo 3D Projectors
CategoriesActive Stereo 3D -- requires expensive and/or bulky shutter glasses. For decades, this has been the standard solution for stereo 3D molecular visualization on the desktop.
Passive Stereo 3D -- requires inexpensive lightweight polarized glasses. This is the standard solution for delivering stereo 3D to audiences of more than a small group of people.
Autostereoscopic 3D -- means that no glasses are required. However, current autostereoscopic displays tend do not to work well for molecular graphics due to their inability to faithfully represent fine detail such as thin bonds and wire meshes.
Active Stereo 3D (High-Refresh) DisplaysThis solution would be analogous to using desktop CRT monitors with shutter glasses. 
LCD Displays (120 Hz)ACER GD235HZ. 1920x1080 120Hz 2ms .
Planar SA2311W. This is a high-end 23' 3D-ready monitor. The resolution is 1900x1280 and has a 2ms refresh time. This worked well for us.
ViewSonic VX2265wm (VX2268wm in Europe) - On the market and verified working under FC 12
Samsung 2233RZ - On the market. Quad buffered stereo in Linux works with a G8x based graphics core or better Quadro FX card with the 3 pin mini din stereo connector (currently, the cheapest card that works in Linux is the Quadro FX 3700), 195.22 (or newer) nvidia linux binary driver, and the Nvidia 3d vision kit. Even though the Quadro FX 1400/3450/4000 cards have a 3 pin stereo connector, these will not work with Nvidia 3D vision since these have core versions less than G8x. For more information see this forum post at the Nvidia Forums. - SP
USB only based stereo with the 3D vision kit works only in MS Windows (e.g. with a low end Quadro FX 370 that has no 3 pin mini din stereo connector). For more information see this forum post at the Nvidia Forums. - SP
The 195.22 Nvidia linux drivers do not support the Samsung 2233RZ in Stereo mode 3 or 10 for quad buffered stereo with other stereo kits, emitters, or goggles such as those purchased from NuVision, Stereographics, or Edimensional. You cannot use NuVision, Stereographics, or Edimensional goggles with the Nvidia 3D Vision emitters. - SP
NVidia 3D NVision kit only supports DirectX software for GeForce (gaming cards) on Windows; users are reporting that they are not able to run PyMOL with NVision with these cards. Get a newer model low end quadro (> G8x graphics core) without the 3 pin mini din (e.g. Quadro 370) or with the 3 pin mini din (e.g. Quadro 3700) for Windows.
NVidia NVision 3D SetupThe NVidia 3D NVision setup provides a very nice 3D experience. You need the following to enable PyMOL to show NVision 3D on Windows. Please review the hardware and software requirements before moving on to the installation and setup.
Necessary HardwareMonitor: 120 Hz LCD: a 2233RZ or a Fuhzion vx2265wm
Cable: Dual Link DVI cable; most 120Hz monitors will come with this cable--regardless, the cable is necessary
Quadro Card: recent Quadro series graphics card (not a GeForce card) such as an FX 380 or 570 or later. The GeForce cards do not support windowed openGL stereo, so we do not support these series of cards for the NVision 3D solution. For linux, you must have a quadro card that has a 3 pin mini din connector. The cheapest/oldest card that will work with linux is the Quadro 3700.WARNING: The Quadro FX1400 does not support 3d vision stereo on Windows7 or Linux.
Emitter: 3D Vision hardware kit (an emitter with 3D shutter glasses). For Linux, make sure your kit comes with the 3 pin mini din 'VESA' to 2.5mm stereo cable to connect from the stereo output on the video card into the emitter. See the 3 pin Mini-DIN connector article for tips on how to make one of these cables if yours is missing.
GeForce Cards from series 400 onward have gained OpenGl support in recent Nvidia driver iterations (314+). This allows Pymol to be viewed in 3D using the quad buffered stereo setting with a GeForce card, 120Hz screen and 3D Vision kit.
Necessary SoftwareWindows XP 32 bit (testing other OSs soon!), Windows Vista
Latest Quadro Drivers from NVidia.
Latest Graphics drivers for the NVision system--under Product Type choose 3D Vision.
Installation InstructionsSystem SetupInstall the Quadro Graphics Drivers and reboot your machines
Install the NVision Installation, hooking up the 3D emitter and glasses as directed in the instructionsMake sure the 3D demos work
Complete the 3D Vision Drivers install (I had errors/warnings about old drivers but this did't matter)
Specify how to drive the 3D by, click on
Windows Start Button > Control Panel > NVidia Control Panel > Manage 3D Settings (tab) > Global Settings (tab on the right) > Base Profile (tab). Then, under Settings choose Stereo - Display Mode. Next, select Generic Active Stereo (with NVidia IR Emitter). If you have a DLP monitor/TV choose the corresponding DLP option. You must also set Stereo - Enable to on.Running PyMOLThat's it! PyMOL should now work in Quad Buffered 3D Stereo using the NVidia 3D NVision system. To run PyMOL in 3D mode on:
Windows
Start > PyMOL > PyMOL > PyMOL 3D Launch (last menu option) > PyMOL Stereo (Quad Buffered 3D)Linux
pymol -S -t 1Note that hardware stereo may not work in Xorg unless window compositing is turned off; Gnome3, Unity, etc all use window compositing as part of their eye candy. A window manager that should work by default is the MATE desktop. Install this if you have troubleMac
MAC InstallSorry, at this time the NVision system is not known to work on Macs.DLP Projection TelevisionsProjection televisions tend to be too large and fuzzy for desktop use. Also, a band of about 20 pixels around on the edge of the display are invisible, and this limitation cannot be eliminated through overscan since the image must be scanned at native resolution in order to support stereo 3D. The workaround is to shrink the PyMOL window to cover the visible portion of the screen. It is worth noting that true 3D-capable LCDs (as distinct from 3D-capable HDTVs) do not suffer from this problem.
Aside from the above concerns, the quality of the DLP stereo 3D effect is exceptional: there is absolutely no ghosting or cross-talk between the two images. 
Samsung 3D-Ready DLP HDTVs - work with PyMOL 1.2b3 & later without any special drivers. Quadro driver support is still lacking as of Feb. 1st, 2009 - WLD
Mitsubishi 3D-Ready DLP HDTVs - not yet tested, but are expected to work with PyMOL 1.2b3 & later without any special drivers. - WLD
See The 3D HDTV List for more 3D-capable HDTV options.
Passive Stereo 3D DisplaysOne Piece Multi-layer LCD DisplaysAffordable!
ZalmaniZ3D, the original supplier of Zalman display drivers has ceased operation and support as of 31 July 2012. DO NOT PURCHASE THESE MONITORS WITHOUT FURTHER CONFIRMATION of display support, the iZ3D support (required drivers, etc) is not activatable. If you do have further information, please post it here.Jedgold 12:21, 12 September 2012 (CDT)
Zalman 22-inch 3D LCD monitor - works with PyMOL 1.2b3 & later without any special drivers. Great stereo quality provided that all drawn lines are at least 2 pixels thick. Menus are a bit awkward to use while in stereo mode, but even so, this 650 USD display provides excellent 3D molecular visualization in both full-screen in windowed modes. - WLD (The Zalman ZM-M220W is DeLano Scientific's RECOMMENDED SOLUTION as of Feb 11, 2009!).
Zalman 24-inch 3D LCD monitor - also works with PyMOL 1.2b3 & later under LINUX (Centos 5 x86_64 plain kernel + NVidia driver from ELRepo). I'm using an NVidia Quadro FX 580 (G96GL) graphics card (£125). Monitor cost around £350. PyMOL automagically detects that quad buffered stereo is available on startup.--Bosmith 16:32, 2 December 2010 (UTC)
LGLG DM2752D This (and other LG passive 3D monitors/TVs) work with PyMOL. I'm driving them using NVidia Quadro 600 graphics cards under LINUX (CentOSes 5, 6 & 7) with the NVidia driver from ELRepo.
On Linuxsetup by editing the xorg.conf file:
in the Device section of xorg.conf add:
in the Screen section of xorg.conf and an additional:
N.B. the current Gnome 3 (gnome-shell) in RHEL 7 derivatives (Scientific, CentOS, etc.) is a compositing window manager and is not properly stereo aware, so you will need to use a different window manager. See e.g. [1] for an alternative.
launch using:
Support | Pymol.orgOn WindowsPymol Free DownloadFrom the Start Menu: In the 'PyMOL' folder, go into the 'Stereo 3D Launch' subfolder, and select 'PyMOL Zalman 3D (By Row)'. You might want to control-drag a copy of that shortcut on to your desktop in order to drag & drop content files onto it for stereo 3D visualization
From the Command Line:
On MacMacPyMOL: Copy and rename the 'MacPyMOL' application bundle to 'MacPyMOLZalman'. You can then double-click on the MacPyMOLZalman icon or drop data files directly onto it to visualize content in the Zalman stereo 3D mode.
PyMOL X11 Hybrid Mode: Copy and rename the 'MacPyMOL' appplication bundle to 'PyMOLX11Zalman'. After launching X11, you can then double-click on the PyMOLX11Zalman icon or drop data files directly onto it to visualize that content in the Zalman stereo 3D mode.
For all platforms, remember to toggle stereo on and off using the 'set stereo' command:
iZ3DIZ3D - works with PyMOL 1.2b3 & later without any special drivers. However, this display exhibits far too much cross-talk and interference between the two stereo images. Not suitable for professional use. - WLD
IZ3D is closed as of 31 July 2012, and will not offer support to their products. Jedgold 12:26, 12 September 2012 (CDT)
Mirror-based Multi-LCD SolutionsDownload avery template 8160 mac. Expensive!
Planar3D 'I have used these displays with nVidia Quadro graphics cards under both Windows and Linux running both PyMOL and Maestro. They work well, and the stereo quality is excellent!' - WLD.
Autostereoscopic LCD DisplaysSome autostereoscopic displays have the ability to switch between 2D and 3D display modes. Others are built for 3D only.
Stereo 3D ProjectorsAlthough these displays require shutter glasses out of the box, when combined with the adapters below and a special 'silvered' screen, they can be used to project Passive Stereo 3D to a large audience.
Active Stereo 3D DLP ProjectorsDepthQ Stereoscopic 'The original DepthQ gave a very good stereo 3D effort with PyMOL, but I haven't seen their latest products.' - WLD.
Christie MIRAGE S+4K SXGA+ 6500 LUMEN DLP™ STEREOSCOPIC PROJECTOR 'I have been very impressed with the stereo 3D effect produced by MIRAGE projectors equipped with StereoGraphic ZScreens running PyMOL under Windows with a high-end nVidia Quadro card.' - WLD.
Passive Stereo 3D Adaptor Hardware for Active Stereo 3D ProjectorsThese devices make it possible for a large audience to see projected stereo 3D using inexpensive polarized glasses.
Who Says What?If you provide a specific quote or endorsement above, please say who you are so that everyone can know the source of the information.
WLD = Warren L. DeLano of DeLano Scientific LLC
SP = Sabuj Pattanayek of the Center For Structural Biology, Vanderbilt University
 Retrieved from 'http://pymolwiki.org/index.php?title=Stereo_3D_Display_Options&oldid=12808' 
A powerful and comprehensive molecular visualization product 
ReviewComments Questions & Answers (1)Update program info
All versionsSee allPyMOL is a comprehensive and powerful application that allows you to design and then visualize molecular structures. It enables the 3D visualization of all kinds of proteins and molecules, together with their related trajectories and surfaces. Since this tool is a very complex one, advanced functions like ray tracing or animating the 3D structures are also supported.
See Full List On Pymolwiki.orgAlthough based on an open source project, a generally-available version of PyMOL that includes additional advantages is offered for a price for non-educational purposes. This version, called 'Incentive PyMOL', includes an installer for Windows (the original open-source PyMOL is a Python-based project which can't be installed just as easy on Windows systems), incentive documentation, user support and handy tutorials, or even built-in tools like a molecular morphing tool. There are also extensive video exporting capabilities that let you create MOV or MPEG video files containing various molecular animations.
PyMOL impresses mostly thanks to its numerous functions and features. It's amazingly powerful and comprehensive but unfortunately it's also not exactly suitable for beginners. Its interface requires spending some time to learn the ropes first.
In conclusion, PyMOL is great especially for experts and professionals that need a powerful and reliable solution to view, render, animate and export 3D molecular structures.
Pros
Very feature-rich and comprehensive
Includes video exporting capabilities
Good rendering speed
Cons
Based on an open-source project yet the generally-available version is not provided for free
Complicated to use for casual users