- Chimera-users - RBVI Mailing Lists

Editing named selections
by Yasser Almeida Hernández 10 Mar '14

10 Mar '14

Hi all, It is possible to edit (rename, remove, etc.) named selections? Regards Yasser -- Yasser Almeida Hernández, MSc. Center of Molecular Immunology (CIM) System Biology Department 216 St. & 15th Ave, Siboney, Playa P.O.Box 16040, Havana 11600 CUBA Phone: (+53-7) 214-3127 almeida(a)cim.sld.cu --------------------------------------------------- [http://5.cim.co.cu/cim.gif]

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Visualizing trajectory
by Yasser Almeida Hernández 10 Mar '14

10 Mar '14

Hi all, I have a MD trajectory from GROMACS and I want to visualize it in Chimera using MD Movie tool. My protein move inside the water box. How I cant fix the protein to see the its dynamics in each frame? I have used VMD for this task, using the RMSD trajectory calculator plugin. Here the trajectory is loaded and then press the Align button. The protein coordinates in each frame is superposed on those from the first frame. Whith this the protein stay in a fixed position. It is this possible in Chimera? On the other hand, It is possible load the trajectory just by every N frames? I have a trajectory with 2 000 000 of frames, and I want to load the trajectory every 100 frames. Thanks in advance Yasser -- Yasser Almeida Hernández, MSc. Center of Molecular Immunology (CIM) System Biology Department 216 St. & 15th Ave, Siboney, Playa P.O.Box 16040, Havana 11600 CUBA Phone: (+53-7) 214-3127 almeida(a)cim.sld.cu --------------------------------------------------- [http://5.cim.co.cu/cim.gif]

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To get CHIMERA to work: "with stereo viz on new samsung "3D" LCD and quadro card"
by Peter Engelhardt 07 Mar '14

07 Mar '14

Dear Chimera, Sorry - Specification - We naturally meant: CHIMERA to WORK with "stereo viz on new samsung "3D" LCD and quadro card" > Dear Chimera, > > We recently got a mail on instruction to install correct parameters > to get VMD-L to work: > > "vmd-l: help with stereo viz on new samsung "3D" LCD and quadro card" > > Now we ask, do you have any suggestions to get "Samsung "3D" LCD and > quadro card" and to get CHIMERA work not only for: > > 1. Linux (Ubuntu) with "quadro card" > > but also and on: > > 2. MacPro/Mavericks with "a quadro card" > > We thank you in advance > > Cheers > Peter et al. > > Quoting John Stone <johns(a)ks.uiuc.edu>: > > [Hide Quoted Text] > Carlos, > Ah, I had missed the startup message you included when I read > your first note. All of the VMD stereo modes other than "QuadBuffered" > are implemented by rendering code within VMD itself, and they do not > depend on the graphics driver or any special hardware capabilities. > So, the fact that you are able to use the "SideBySide" or other modes > just indicates that your TV can work with the VMD-supplied mode, but > that's separate from the issue of having the Quadro's stereo sync and > other features working. > > The VMD "QuadBuffered" stereo mode relies entirely on the GPU and > its driver for stereoscopic display. This is the best mode to use > if you want the IR or RF stereo emitter to remain in proper sync with > the displayed images, but it requires that the GPU drivers and windowing > system be configured correctly, and that the GPU and driver will actually > support the target display. If you're running on Linux, then the thing > to do is to check the contents of /var/log/Xorg.0.log and look for > the word "Stereo". Here's an example of the kinds of output you're looking > for, as seen on a couple of our machines: > (**) NVIDIA(1): Option "Stereo" "10" > (**) NVIDIA(1): Option "ForceStereoFlipping" "true" > > Here's a machine that has stereo enabled: > (II) Setting vga for screen 0. > (II) Setting vga for screen 1. > (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(0): RGB weight 888 > (==) NVIDIA(0): Default visual is TrueColor > (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(0): Option "MetaModes" "2560x1600 +0+0" > (**) Feb 17 16:21:29 NVIDIA(0): Enabling 2D acceleration > (II) Feb 17 16:21:29 NVIDIA(0): Display (Samsung SyncMaster (DFP-0)) > does not support NVIDIA > (II) Feb 17 16:21:29 NVIDIA(0): 3D Vision stereo. > (II) Feb 17 16:21:29 NVIDIA(0): NVIDIA GPU Quadro 7000 (GF110GL) at > PCI:8:0:0 (GPU-0) > (--) Feb 17 16:21:29 NVIDIA(0): Memory: 6291456 kBytes > (--) Feb 17 16:21:29 NVIDIA(0): VideoBIOS: 70.10.4a.00.01 > (II) Feb 17 16:21:29 NVIDIA(0): Detected PCI Express Link width: 16X > (--) Feb 17 16:21:29 NVIDIA(0): Valid display device(s) on Quadro > 7000 at PCI:8:0:0 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-0 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-1 > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0) > (boot, connected) > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): CRT-1: 400.0 MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): Internal > Dual Link TMDS > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): 330.0 > MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: Internal Single Link TMDS > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: 330.0 MHz maximum pixel clock > (**) Feb 17 16:21:29 NVIDIA(0): Using HorizSync/VertRefresh ranges > from the EDID for display > (**) Feb 17 16:21:29 NVIDIA(0): device Samsung SyncMaster > (DFP-0) (Using EDID frequencies > (**) Feb 17 16:21:29 NVIDIA(0): has been enabled on all display devices.) > (II) Feb 17 16:21:29 NVIDIA(0): Validated MetaModes: > (II) Feb 17 16:21:29 NVIDIA(0): "2560x1600+0+0" > (II) Feb 17 16:21:29 NVIDIA(0): Virtual screen size determined to be > 2560 x 1600 > (--) Feb 17 16:21:29 NVIDIA(0): DPI set to (101, 101); computed from > "UseEdidDpi" X config > (--) Feb 17 16:21:29 NVIDIA(0): option > (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(1): RGB weight 888 > (==) NVIDIA(1): Default visual is TrueColor > (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(1): Option "Stereo" "10" > (**) NVIDIA(1): Option "ForceStereoFlipping" "true" > (**) Feb 17 16:21:29 NVIDIA(1): USB IR emitter stereo requested > (WW) Feb 17 16:21:29 NVIDIA(1): For stereo to work with Xinerama, > stereo X configuration > (WW) Feb 17 16:21:29 NVIDIA(1): option should be enabled on all > X screens in the X server. > (WW) Feb 17 16:21:29 NVIDIA(1): Stereo is disabled on one (or > more) X screens, while > (WW) Feb 17 16:21:29 NVIDIA(1): Xinerama is enabled. Stereo > visuals will not be > (WW) Feb 17 16:21:29 NVIDIA(1): available. > (**) Feb 17 16:21:29 NVIDIA(1): OpenGL stereo forced > (**) NVIDIA(1): Option "MetaModes" "nvidia-auto-select +0+0" > (**) Feb 17 16:21:29 NVIDIA(1): Enabling 2D acceleration > (II) Feb 17 16:21:29 NVIDIA(0): Display (Acer HN274H (DFP-0)) > supports NVIDIA 3D Vision > (II) Feb 17 16:21:29 NVIDIA(0): stereo. > (II) Feb 17 16:21:29 NVIDIA(1): NVIDIA GPU Quadro 7000 (GF110GL) at > PCI:9:0:0 (GPU-1) > (--) Feb 17 16:21:29 NVIDIA(1): Memory: 6291456 kBytes > > > Here's a machine that has stereo disabled currently: > (II) Setting vga for screen 0. > (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(0): RGB weight 888 > (==) NVIDIA(0): Default visual is TrueColor > (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(0): Option "Stereo" "0" > (**) NVIDIA(0): Option "nvidiaXineramaInfoOrder" "DFP-3" > (**) Feb 17 17:20:19 NVIDIA(0): Stereo disabled by request > (**) NVIDIA(0): Option "MetaModes" "DFP-0: nvidia-auto-select > +2560+520, DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +2560+0, > DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +0+0, DFP-3: > nvidia-auto-select +1920+0" > (**) Feb 17 17:20:19 NVIDIA(0): Enabling 2D acceleration > (II) Feb 17 17:20:21 NVIDIA(0): Display (Acer HN274H (DFP-0)) > supports NVIDIA 3D Vision > (II) Feb 17 17:20:21 NVIDIA(0): stereo. > (II) Feb 17 17:20:21 NVIDIA(0): Display (HP ZR30w (DFP-3)) does not > support NVIDIA 3D Vision > (II) Feb 17 17:20:21 NVIDIA(0): stereo. > (II) Feb 17 17:20:21 NVIDIA(0): NVIDIA GPU Quadro K6000 (GK110BGL) > at PCI:131:0:0 (GPU-0) > (--) Feb 17 17:20:21 NVIDIA(0): Memory: 12582912 kBytes > (--) Feb 17 17:20:21 NVIDIA(0): VideoBIOS: 80.80.16.00.01 > (II) Feb 17 17:20:21 NVIDIA(0): Detected PCI Express Link width: 16X > (--) Feb 17 17:20:21 NVIDIA(0): Valid display device(s) on Quadro > K6000 at PCI:131:0:0 > (--) Feb 17 17:20:21 NVIDIA(0): CRT-0 > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0) (boot, connected) > (--) Feb 17 17:20:21 NVIDIA(0): DFP-1 > (--) Feb 17 17:20:21 NVIDIA(0): DFP-2 > (--) Feb 17 17:20:21 NVIDIA(0): HP ZR30w (DFP-3) (connected) > (--) Feb 17 17:20:21 NVIDIA(0): DFP-4 > (--) Feb 17 17:20:21 NVIDIA(0): DFP-5 > (--) Feb 17 17:20:21 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): Internal Dual Link TMDS > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): 330.0 MHz > maximum pixel clo > -- ___________________________________________________________ Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/ Department of Pathology lab. tel: (+358-9)-19126729, 19126442 EM-lab, Tel: (+358-9)-19126261 Fax: (+358-9)-19126700 (Dept. of Pathology) Nanomicroscopy Center, Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358400193342

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CHIMERA: help with stereo viz on new samsung "3D" LCD and quadro card
by Peter Engelhardt 07 Mar '14

07 Mar '14

Sorry2 for a typo - now corrected: Dear Chimera, We recently got a mail on instruction to install correct parameters to get VMD-L to work: "vmd-l: help with stereo viz on new samsung "3D" LCD and quadro card" Now we ask, do you have any suggestions to get "Samsung "3D" LCD and quadro card" to work - not only for: 1. Linux (Ubuntu) with "quadro card" but also and on: 2. MacPro/Mavericks with "a quadro card" We thank you in advance Cheers Peter et al. Quoting John Stone <johns(a)ks.uiuc.edu>: [Hide Quoted Text] Carlos, Ah, I had missed the startup message you included when I read your first note. All of the VMD stereo modes other than "QuadBuffered" are implemented by rendering code within VMD itself, and they do not depend on the graphics driver or any special hardware capabilities. So, the fact that you are able to use the "SideBySide" or other modes just indicates that your TV can work with the VMD-supplied mode, but that's separate from the issue of having the Quadro's stereo sync and other features working. The VMD "QuadBuffered" stereo mode relies entirely on the GPU and its driver for stereoscopic display. This is the best mode to use if you want the IR or RF stereo emitter to remain in proper sync with the displayed images, but it requires that the GPU drivers and windowing system be configured correctly, and that the GPU and driver will actually support the target display. If you're running on Linux, then the thing to do is to check the contents of /var/log/Xorg.0.log and look for the word "Stereo". Here's an example of the kinds of output you're looking for, as seen on a couple of our machines: (**) NVIDIA(1): Option "Stereo" "10" (**) NVIDIA(1): Option "ForceStereoFlipping" "true" Here's a machine that has stereo enabled: (II) Setting vga for screen 0. (II) Setting vga for screen 1. (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(0): RGB weight 888 (==) NVIDIA(0): Default visual is TrueColor (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(0): Option "MetaModes" "2560x1600 +0+0" (**) Feb 17 16:21:29 NVIDIA(0): Enabling 2D acceleration (II) Feb 17 16:21:29 NVIDIA(0): Display (Samsung SyncMaster (DFP-0)) does not support NVIDIA (II) Feb 17 16:21:29 NVIDIA(0): 3D Vision stereo. (II) Feb 17 16:21:29 NVIDIA(0): NVIDIA GPU Quadro 7000 (GF110GL) at PCI:8:0:0 (GPU-0) (--) Feb 17 16:21:29 NVIDIA(0): Memory: 6291456 kBytes (--) Feb 17 16:21:29 NVIDIA(0): VideoBIOS: 70.10.4a.00.01 (II) Feb 17 16:21:29 NVIDIA(0): Detected PCI Express Link width: 16X (--) Feb 17 16:21:29 NVIDIA(0): Valid display device(s) on Quadro 7000 at PCI:8:0:0 (--) Feb 17 16:21:29 NVIDIA(0): CRT-0 (--) Feb 17 16:21:29 NVIDIA(0): CRT-1 (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0) (boot, connected) (--) Feb 17 16:21:29 NVIDIA(0): DFP-1 (--) Feb 17 16:21:29 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock (--) Feb 17 16:21:29 NVIDIA(0): CRT-1: 400.0 MHz maximum pixel clock (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): Internal Dual Link TMDS (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): 330.0 MHz maximum pixel clock (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: Internal Single Link TMDS (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: 330.0 MHz maximum pixel clock (**) Feb 17 16:21:29 NVIDIA(0): Using HorizSync/VertRefresh ranges from the EDID for display (**) Feb 17 16:21:29 NVIDIA(0): device Samsung SyncMaster (DFP-0) (Using EDID frequencies (**) Feb 17 16:21:29 NVIDIA(0): has been enabled on all display devices.) (II) Feb 17 16:21:29 NVIDIA(0): Validated MetaModes: (II) Feb 17 16:21:29 NVIDIA(0): "2560x1600+0+0" (II) Feb 17 16:21:29 NVIDIA(0): Virtual screen size determined to be 2560 x 1600 (--) Feb 17 16:21:29 NVIDIA(0): DPI set to (101, 101); computed from "UseEdidDpi" X config (--) Feb 17 16:21:29 NVIDIA(0): option (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(1): RGB weight 888 (==) NVIDIA(1): Default visual is TrueColor (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(1): Option "Stereo" "10" (**) NVIDIA(1): Option "ForceStereoFlipping" "true" (**) Feb 17 16:21:29 NVIDIA(1): USB IR emitter stereo requested (WW) Feb 17 16:21:29 NVIDIA(1): For stereo to work with Xinerama, stereo X configuration (WW) Feb 17 16:21:29 NVIDIA(1): option should be enabled on all X screens in the X server. (WW) Feb 17 16:21:29 NVIDIA(1): Stereo is disabled on one (or more) X screens, while (WW) Feb 17 16:21:29 NVIDIA(1): Xinerama is enabled. Stereo visuals will not be (WW) Feb 17 16:21:29 NVIDIA(1): available. (**) Feb 17 16:21:29 NVIDIA(1): OpenGL stereo forced (**) NVIDIA(1): Option "MetaModes" "nvidia-auto-select +0+0" (**) Feb 17 16:21:29 NVIDIA(1): Enabling 2D acceleration (II) Feb 17 16:21:29 NVIDIA(0): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision (II) Feb 17 16:21:29 NVIDIA(0): stereo. (II) Feb 17 16:21:29 NVIDIA(1): NVIDIA GPU Quadro 7000 (GF110GL) at PCI:9:0:0 (GPU-1) (--) Feb 17 16:21:29 NVIDIA(1): Memory: 6291456 kBytes Here's a machine that has stereo disabled currently: (II) Setting vga for screen 0. (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(0): RGB weight 888 (==) NVIDIA(0): Default visual is TrueColor (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(0): Option "Stereo" "0" (**) NVIDIA(0): Option "nvidiaXineramaInfoOrder" "DFP-3" (**) Feb 17 17:20:19 NVIDIA(0): Stereo disabled by request (**) NVIDIA(0): Option "MetaModes" "DFP-0: nvidia-auto-select +2560+520, DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +2560+0, DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +0+0, DFP-3: nvidia-auto-select +1920+0" (**) Feb 17 17:20:19 NVIDIA(0): Enabling 2D acceleration (II) Feb 17 17:20:21 NVIDIA(0): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision (II) Feb 17 17:20:21 NVIDIA(0): stereo. (II) Feb 17 17:20:21 NVIDIA(0): Display (HP ZR30w (DFP-3)) does not support NVIDIA 3D Vision (II) Feb 17 17:20:21 NVIDIA(0): stereo. (II) Feb 17 17:20:21 NVIDIA(0): NVIDIA GPU Quadro K6000 (GK110BGL) at PCI:131:0:0 (GPU-0) (--) Feb 17 17:20:21 NVIDIA(0): Memory: 12582912 kBytes (--) Feb 17 17:20:21 NVIDIA(0): VideoBIOS: 80.80.16.00.01 (II) Feb 17 17:20:21 NVIDIA(0): Detected PCI Express Link width: 16X (--) Feb 17 17:20:21 NVIDIA(0): Valid display device(s) on Quadro K6000 at PCI:131:0:0 (--) Feb 17 17:20:21 NVIDIA(0): CRT-0 (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0) (boot, connected) (--) Feb 17 17:20:21 NVIDIA(0): DFP-1 (--) Feb 17 17:20:21 NVIDIA(0): DFP-2 (--) Feb 17 17:20:21 NVIDIA(0): HP ZR30w (DFP-3) (connected) (--) Feb 17 17:20:21 NVIDIA(0): DFP-4 (--) Feb 17 17:20:21 NVIDIA(0): DFP-5 (--) Feb 17 17:20:21 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): Internal Dual Link TMDS (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): 330.0 MHz maximum pixel clo On Tue, Feb 18, 2014 at 08:06:04AM -0500, Carlos Simmerling wrote: Hi John, thanks for the quick reply. I included VMD's output in my original post- yes, it says stereo, and I can indeed get VMD to do stereo if I pick side by side mode in VMD. I'm using win 7 pro (though I'd upgrade to win 8 if I knew that would solve the problem). The TV is HDMI only, unfortunately. The quadro card has only DVI outputs, so I'm using a DVI to HDMI cable. I'm hoping to find a way to do quad buffered stereo at a reasonable refresh rate. Carlos On Mon, Feb 17, 2014 at 12:53 PM, John Stone <johns(a)ks.uiuc.edu> wrote: Hi Carlos, I'm not familiar with the TV you're using, but I can say a few things that are broadly true of a wide range of HDTVs that support stereo that may also apply in your case. If a TV has a DVI input (unlikely), then one is sometimes able to use it just like any other stereo display. If the TV uses HDMI, then the options for stereo will depend somewhat on which operating system the computer is running what video card, and what driver are being used. In regards to the NVIDIA GPUs, the "Quadro" GPUs have the best support for stereoscopic display across all OS platforms. Last I knew however, HDTVs are considered a special case, and at least on the Windows platform there was/is a special driver that one had to use to allow stereoscopic display to an HDTV over HDMI (3DTV Play) for games and the like: http://www.nvidia.com/object/3dtv-play-overview.html I just looked up the NVIDIA web site regarding stereoscopic display, and they have clearly rewritten much of it since the last time I looked: http://www.nvidia.com/object/3d-vision-professional-users.html I would expect that the Quadro would have a good chance of working with a 3D HDTV, but you will likely have to set the NVIDIA driver's stereo mode to one that your TV agrees with. If you tell me which OS you're running, we can work through a few of the details there. The most important thing is to see if VMD lists "STEREO" during the OpenGL feature startup messages that it prints to the text console. Cheers, John Stone vmd(a)ks.uiuc.edu On Fri, Feb 14, 2014 at 02:25:25PM -0500, Carlos Simmerling wrote: Hi all, I'm trying to optimize my stereo viewing. I have windows 7 pro, a quadro fx-4600 and a samsung UN60F8000BF LCD TV (http://www.samsung.com/us/video/tvs/UN60F8000BFXZA) that came with active stereo glasses. I also have an old stereographics emitter with 3-pin DIN connector that plugs into my quadro card, along with some stereographics glasses. VMD tells me this at startup: Info) OpenGL renderer: Quadro FX 4600/PCIe/SSE2 Info) Features: STENCIL STEREO MDE CVA MTX NPOT PP PS GLSL(OVF) So, what I need help with is optimizing my 3D viewing. So far I can only get this setup to work when I select side by side 3D in VMD, and on the TV I also select side by side and use the glasses that came with it. It's ok, but the glasses are cheap and there's some bleed through, and of course I lose resolution. I suspect I'd be better off using the emitter and the expensive SG glasses. When I plug in the emitter, the red light goes on so it seems to be working. If I select stereo/quadbuffered in VMD, it looks like it's doing the right thing, but using the SG glasses doesn't seem to sync properly. A few other questions: 1) do the settings in the Nvidia control panel under "manage 3D settings" impact VMD? In there you can choose the 3D mode, antialiasing, etc. I don't know if that controls the openGL part. 2) Is it possible to send a >60HZ signal to these screens? It claims it is 240Hz, but I don't know if that's internal interpolation or accepts inputs >60Hz. thanks! -- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/ -- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/ -- -- ___________________________________________________________ Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/ Department of Pathology lab. tel: (+358-9)-19126729, 19126442 EM-lab, Tel: (+358-9)-19126261 Fax: (+358-9)-19126700 (Dept. of Pathology) Nanomicroscopy Center, Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358400193342

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CHIMERA: help with stereo viz on new samsung "3D" LCD and quadro card
by Peter Engelhardt 07 Mar '14

07 Mar '14

Sorry for the earlier mail the body text was not correct here a new mail with the original vmd-l mail included (see below) Dear Chimera, We recently got a mail on instruction to install correct parameters to get VMD-L to work: "vmd-l: help with stereo viz on new samsung "3D" LCD and quadro card" Now we ask, do you have any suggestion how to get "Samsung "3D" LCD and quadro card not to work - not only for: 1. Linux (Ubuntu) with "quadro card" but also and on: 2. MacPro/Mavericks with "a quadro card" We thank you in advance Cheers Peter et al. Quoting John Stone <johns(a)ks.uiuc.edu>: > Carlos, > Ah, I had missed the startup message you included when I read > your first note. All of the VMD stereo modes other than "QuadBuffered" > are implemented by rendering code within VMD itself, and they do not > depend on the graphics driver or any special hardware capabilities. > So, the fact that you are able to use the "SideBySide" or other modes > just indicates that your TV can work with the VMD-supplied mode, but > that's separate from the issue of having the Quadro's stereo sync and > other features working. > > The VMD "QuadBuffered" stereo mode relies entirely on the GPU and > its driver for stereoscopic display. This is the best mode to use > if you want the IR or RF stereo emitter to remain in proper sync with > the displayed images, but it requires that the GPU drivers and windowing > system be configured correctly, and that the GPU and driver will actually > support the target display. If you're running on Linux, then the thing > to do is to check the contents of /var/log/Xorg.0.log and look for > the word "Stereo". Here's an example of the kinds of output you're looking > for, as seen on a couple of our machines: > (**) NVIDIA(1): Option "Stereo" "10" > (**) NVIDIA(1): Option "ForceStereoFlipping" "true" > > Here's a machine that has stereo enabled: > (II) Setting vga for screen 0. > (II) Setting vga for screen 1. > (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(0): RGB weight 888 > (==) NVIDIA(0): Default visual is TrueColor > (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(0): Option "MetaModes" "2560x1600 +0+0" > (**) Feb 17 16:21:29 NVIDIA(0): Enabling 2D acceleration > (II) Feb 17 16:21:29 NVIDIA(0): Display (Samsung SyncMaster (DFP-0)) > does not support NVIDIA > (II) Feb 17 16:21:29 NVIDIA(0): 3D Vision stereo. > (II) Feb 17 16:21:29 NVIDIA(0): NVIDIA GPU Quadro 7000 (GF110GL) at > PCI:8:0:0 (GPU-0) > (--) Feb 17 16:21:29 NVIDIA(0): Memory: 6291456 kBytes > (--) Feb 17 16:21:29 NVIDIA(0): VideoBIOS: 70.10.4a.00.01 > (II) Feb 17 16:21:29 NVIDIA(0): Detected PCI Express Link width: 16X > (--) Feb 17 16:21:29 NVIDIA(0): Valid display device(s) on Quadro > 7000 at PCI:8:0:0 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-0 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-1 > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0) > (boot, connected) > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): CRT-1: 400.0 MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): Internal > Dual Link TMDS > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): 330.0 > MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: Internal Single Link TMDS > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: 330.0 MHz maximum pixel clock > (**) Feb 17 16:21:29 NVIDIA(0): Using HorizSync/VertRefresh ranges > from the EDID for display > (**) Feb 17 16:21:29 NVIDIA(0): device Samsung SyncMaster > (DFP-0) (Using EDID frequencies > (**) Feb 17 16:21:29 NVIDIA(0): has been enabled on all display devices.) > (II) Feb 17 16:21:29 NVIDIA(0): Validated MetaModes: > (II) Feb 17 16:21:29 NVIDIA(0): "2560x1600+0+0" > (II) Feb 17 16:21:29 NVIDIA(0): Virtual screen size determined to be > 2560 x 1600 > (--) Feb 17 16:21:29 NVIDIA(0): DPI set to (101, 101); computed from > "UseEdidDpi" X config > (--) Feb 17 16:21:29 NVIDIA(0): option > (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(1): RGB weight 888 > (==) NVIDIA(1): Default visual is TrueColor > (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(1): Option "Stereo" "10" > (**) NVIDIA(1): Option "ForceStereoFlipping" "true" > (**) Feb 17 16:21:29 NVIDIA(1): USB IR emitter stereo requested > (WW) Feb 17 16:21:29 NVIDIA(1): For stereo to work with Xinerama, > stereo X configuration > (WW) Feb 17 16:21:29 NVIDIA(1): option should be enabled on all > X screens in the X server. > (WW) Feb 17 16:21:29 NVIDIA(1): Stereo is disabled on one (or > more) X screens, while > (WW) Feb 17 16:21:29 NVIDIA(1): Xinerama is enabled. Stereo > visuals will not be > (WW) Feb 17 16:21:29 NVIDIA(1): available. > (**) Feb 17 16:21:29 NVIDIA(1): OpenGL stereo forced > (**) NVIDIA(1): Option "MetaModes" "nvidia-auto-select +0+0" > (**) Feb 17 16:21:29 NVIDIA(1): Enabling 2D acceleration > (II) Feb 17 16:21:29 NVIDIA(0): Display (Acer HN274H (DFP-0)) > supports NVIDIA 3D Vision > (II) Feb 17 16:21:29 NVIDIA(0): stereo. > (II) Feb 17 16:21:29 NVIDIA(1): NVIDIA GPU Quadro 7000 (GF110GL) at > PCI:9:0:0 (GPU-1) > (--) Feb 17 16:21:29 NVIDIA(1): Memory: 6291456 kBytes > > > > > > > Here's a machine that has stereo disabled currently: > (II) Setting vga for screen 0. > (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(0): RGB weight 888 > (==) NVIDIA(0): Default visual is TrueColor > (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(0): Option "Stereo" "0" > (**) NVIDIA(0): Option "nvidiaXineramaInfoOrder" "DFP-3" > (**) Feb 17 17:20:19 NVIDIA(0): Stereo disabled by request > (**) NVIDIA(0): Option "MetaModes" "DFP-0: nvidia-auto-select > +2560+520, DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +2560+0, > DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +0+0, DFP-3: > nvidia-auto-select +1920+0" > (**) Feb 17 17:20:19 NVIDIA(0): Enabling 2D acceleration > (II) Feb 17 17:20:21 NVIDIA(0): Display (Acer HN274H (DFP-0)) > supports NVIDIA 3D Vision > (II) Feb 17 17:20:21 NVIDIA(0): stereo. > (II) Feb 17 17:20:21 NVIDIA(0): Display (HP ZR30w (DFP-3)) does not > support NVIDIA 3D Vision > (II) Feb 17 17:20:21 NVIDIA(0): stereo. > (II) Feb 17 17:20:21 NVIDIA(0): NVIDIA GPU Quadro K6000 (GK110BGL) > at PCI:131:0:0 (GPU-0) > (--) Feb 17 17:20:21 NVIDIA(0): Memory: 12582912 kBytes > (--) Feb 17 17:20:21 NVIDIA(0): VideoBIOS: 80.80.16.00.01 > (II) Feb 17 17:20:21 NVIDIA(0): Detected PCI Express Link width: 16X > (--) Feb 17 17:20:21 NVIDIA(0): Valid display device(s) on Quadro > K6000 at PCI:131:0:0 > (--) Feb 17 17:20:21 NVIDIA(0): CRT-0 > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0) (boot, connected) > (--) Feb 17 17:20:21 NVIDIA(0): DFP-1 > (--) Feb 17 17:20:21 NVIDIA(0): DFP-2 > (--) Feb 17 17:20:21 NVIDIA(0): HP ZR30w (DFP-3) (connected) > (--) Feb 17 17:20:21 NVIDIA(0): DFP-4 > (--) Feb 17 17:20:21 NVIDIA(0): DFP-5 > (--) Feb 17 17:20:21 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): Internal Dual Link TMDS > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): 330.0 MHz > maximum pixel clo > > > On Tue, Feb 18, 2014 at 08:06:04AM -0500, Carlos Simmerling wrote: >> Hi John, >> thanks for the quick reply. >> I included VMD's output in my original post- yes, it says stereo, and >> I can indeed get VMD to do stereo if I pick side by side mode in VMD. >> I'm using win 7 pro (though I'd upgrade to win 8 if I knew that would >> solve the problem). The TV is HDMI only, unfortunately. The quadro >> card has only DVI outputs, so I'm using a DVI to HDMI cable. >> >> I'm hoping to find a way to do quad buffered stereo at a reasonable >> refresh rate. >> Carlos >> >> On Mon, Feb 17, 2014 at 12:53 PM, John Stone <johns(a)ks.uiuc.edu> wrote: >> > Hi Carlos, >> > I'm not familiar with the TV you're using, but I can say a few >> > things that are broadly true of a wide range of HDTVs that support >> > stereo that may also apply in your case. >> > >> > If a TV has a DVI input (unlikely), then one is sometimes able to use it >> > just like any other stereo display. >> > >> > If the TV uses HDMI, then the options for stereo will depend >> > somewhat on which operating system the computer is running what >> > video card, and what driver are being used. >> > >> > In regards to the NVIDIA GPUs, the "Quadro" GPUs have the best support >> > for stereoscopic display across all OS platforms. Last I knew however, >> > HDTVs are considered a special case, and at least on the Windows platform >> > there was/is a special driver that one had to use to allow stereoscopic >> > display to an HDTV over HDMI (3DTV Play) for games and the like: >> > http://www.nvidia.com/object/3dtv-play-overview.html >> > >> > I just looked up the NVIDIA web site regarding stereoscopic display, >> > and they have clearly rewritten much of it since the last time I looked: >> > http://www.nvidia.com/object/3d-vision-professional-users.html >> > >> > I would expect that the Quadro would have a good chance of working with >> > a 3D HDTV, but you will likely have to set the NVIDIA driver's stereo >> > mode to one that your TV agrees with. If you tell me which OS >> > you're running, we can work through a few of the details there. >> > The most important thing is to see if VMD lists "STEREO" during the >> > OpenGL feature startup messages that it prints to the text console. >> > >> > Cheers, >> > John Stone >> > vmd(a)ks.uiuc.edu >> > >> > On Fri, Feb 14, 2014 at 02:25:25PM -0500, Carlos Simmerling wrote: >> >> Hi all, >> >> >> >> I'm trying to optimize my stereo viewing. >> >> I have windows 7 pro, a quadro fx-4600 and a samsung UN60F8000BF LCD >> >> TV (http://www.samsung.com/us/video/tvs/UN60F8000BFXZA) that came with >> >> active stereo glasses. I also have an old stereographics emitter with >> >> 3-pin DIN connector that plugs into my quadro card, along with some >> >> stereographics glasses. VMD tells me this at startup: >> >> Info) OpenGL renderer: Quadro FX 4600/PCIe/SSE2 >> >> Info) Features: STENCIL STEREO MDE CVA MTX NPOT PP PS GLSL(OVF) >> >> >> >> So, what I need help with is optimizing my 3D viewing. So far I can >> >> only get this setup to work when I select side by side 3D in VMD, and >> >> on the TV I also select side by side and use the glasses that came >> >> with it. It's ok, but the glasses are cheap and there's some bleed >> >> through, and of course I lose resolution. >> >> >> >> I suspect I'd be better off using the emitter and the expensive SG >> >> glasses. When I plug in the emitter, the red light goes on so it seems >> >> to be working. If I select stereo/quadbuffered in VMD, it looks like >> >> it's doing the right thing, but using the SG glasses doesn't seem to >> >> sync properly. >> >> >> >> A few other questions: >> >> 1) do the settings in the Nvidia control panel under "manage 3D >> >> settings" impact VMD? In there you can choose the 3D mode, >> >> antialiasing, etc. I don't know if that controls the openGL part. >> >> 2) Is it possible to send a >60HZ signal to these screens? It claims >> >> it is 240Hz, but I don't know if that's internal interpolation or >> >> accepts inputs >60Hz. >> >> >> >> thanks! >> > >> > -- >> > NIH Center for Macromolecular Modeling and Bioinformatics >> > Beckman Institute for Advanced Science and Technology >> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 >> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 >> > http://www.ks.uiuc.edu/Research/vmd/ > > -- > NIH Center for Macromolecular Modeling and Bioinformatics > Beckman Institute for Advanced Science and Technology > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 > http://www.ks.uiuc.edu/Research/vmd/ -- ___________________________________________________________ Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/ Department of Pathology lab. tel: (+358-9)-19126729, 19126442 EM-lab, Tel: (+358-9)-19126261 Fax: (+358-9)-19126700 (Dept. of Pathology) Nanomicroscopy Center, Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358400193342

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Re: [Chimera-users] Chimera-users Digest, Vol 131, Issue 5
by Peter Engelhardt 07 Mar '14

07 Mar '14

Dear Chimera, We recently got a mail on instruction to install correct parameters to get VMD-L to work: "vmd-l: help with stereo viz on new samsung "3D" LCD and quadro card" Now we ask, do you have any suggestion how to get "Samsung "3D" LCD and quadro card not to work - not only for: 1. Linux (Ubuntu) with "quadro card" but also and on: 2. MacPro/Mavericks with "a quadro card" We thank you in advance Cheers Peter et al. Quoting chimera-users-request(a)cgl.ucsf.edu: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. surface failures (Julian Marzi) > 2. Re: surface failures (Elaine Meng) > 3. Area/Volume from Web not working (Hurt, Darrell (NIH/NIAID) [E]) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 4 Mar 2014 12:31:46 +0100 > From: Julian Marzi <julian.marzi(a)googlemail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] surface failures > Message-ID: <F372C2E9-7034-47D3-B94A-CBE2D6DEF470(a)googlemail.com> > Content-Type: text/plain; charset=us-ascii > > Dear Chimera, > > I try to show the surface of the 60S in yeast (PDB: 3O5H), but it > doesn't work. Mscalc returned code 11 is shown. If I split the 60S > every chain show the surface except the first strain (25S). How can > I show the surface from the first chain? > > Thank you very much > > Best regards > > Julian Marzi > > > ------------------------------ > > Message: 2 > Date: Thu, 6 Mar 2014 10:20:22 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Julian Marzi <julian.marzi(a)googlemail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] surface failures > Message-ID: <E468C80B-D21F-40B7-A569-B66126212530(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Dear Julian, > The surface failure is a numerical thing that may differ on > different machines, and there is not a consistent recipe for how to > solve the problem. Please see this page on possible solutions, > including showing some alternative types of surface instead of a > "molecular" surface: > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Mar 4, 2014, at 3:31 AM, Julian Marzi <julian.marzi(a)googlemail.com> wrote: > >> Dear Chimera, >> I try to show the surface of the 60S in yeast (PDB: 3O5H), but it >> doesn't work. Mscalc returned code 11 is shown. If I split the 60S >> every chain show the surface except the first strain (25S). How can >> I show the surface from the first chain? >> Thank you very much >> Best regards >> Julian Marzi > > > > > ------------------------------ > > Message: 3 > Date: Thu, 6 Mar 2014 19:48:26 +0000 > From: "Hurt, Darrell (NIH/NIAID) [E]" <darrellh(a)niaid.nih.gov> > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] Area/Volume from Web not working > Message-ID: <CF3E3B45.E956%darrellh(a)niaid.nih.gov> > Content-Type: text/plain; charset="us-ascii" > > Hi Chimera friends, > > I'm trying to use "Area/Volume from Web", but I keep getting an > error about how the server is not giving the expected output. > > I'm using build 39297. > > Any hints? > > Thanks, > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home > Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> > Twitter: @niaidbioit<https://twitter.com/niaidbioit> > > Disclaimer: The information in this e-mail and any of its > attachments is confidential and may contain sensitive information. > It should not be used by anyone who is not the original intended > recipient. If you have received this e-mail in error please inform > the sender and delete it from your mailbox or any other storage > devices. National Institute of Allergy and Infectious Diseases shall > not accept liability for any statements made that are sender's own > and not expressly made on behalf of the NIAID by one of its > representatives. > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 131, Issue 5 > ********************************************* -- ___________________________________________________________ Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/ Department of Pathology lab. tel: (+358-9)-19126729, 19126442 EM-lab, Tel: (+358-9)-19126261 Fax: (+358-9)-19126700 (Dept. of Pathology) Nanomicroscopy Center, Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358400193342

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Area/Volume from Web not working
by Hurt, Darrell (NIH/NIAID) [E] 06 Mar '14

06 Mar '14

Hi Chimera friends, I'm trying to use "Area/Volume from Web", but I keep getting an error about how the server is not giving the expected output. I'm using build 39297. Any hints? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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superimposition of DNA moleucles
by Urszula Uciechowska 05 Mar '14

05 Mar '14

Dear chimera users, I need to supeimpose a DNA molecule DNA-1.pdb into the protein-DNA complex. I was trying to do this using Mach Maker, but I am getting errors. I am not sure if I can do it using this tool and how should I do it. Thank you in advance for any help and suggestions... best regards Urszula ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/

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exported as PDB, but structure is not the same upon reopening
by Stern, Alexander Thomas 03 Mar '14

03 Mar '14

Hello, I am attempting to attach a covalent (cysteine modifying) ligand to my protein, and I will later be optimizing/minimizing in another program. I opened my structure in Chimera, loaded the ligands, moved them roughly into place, and merged the models. I then added the bonds and exported the file as a pdb. Upon reopening that very same pdb in Chimera, the bonds I made are gone (however, the ligands are in the position I placed them in). Curious to understand what I am doing incorrectly here. Alex The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Building protein-protein complex with known interacting residues
by fei.wu＠chem.utah.edu 03 Mar '14

03 Mar '14

Dear Chimera Team, I am studying the interactions between three enzymes with their biological assembly structures available in PDB. Using mass spectrometry, I have been able to identify interfacial residues, and what I want to do is build up a super complex (made of the three proteins) in a desired way that these proteins are oriented by interactions between experimentally-determined residues. Would you please tell me that, if I can make or draw this in chimera? And I am also trying to compare experimentally-proposed complex structure with simulated structure. Is there a specific way in chimera to simulate interactions between two or more proteins? I found that when I opened multiple protein files in one session, chimera would gave me a complex of these proteins (not always true with different pdb files). Is this an automatic generation of simulated protein complexes or just a superimposition of part of proteins? Thanks, Fei -- Fei Wu, Ph.D. candidate Shelley D. Minteer Group Chemistry Department University of Utah Phone: 385-234-0603 Email: fei.wu(a)chem.utah.edu

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