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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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Expanding EMdatabank map to full map
by Jason C Porta 03 Mar '14

03 Mar '14

Greetings, I am searching for a way to take a map from the EMdatabank which is just a cut-out of an icosahedral asymmetric and generate the full map via the sym operators. I see there are similar options for generating sym-related models, but is there a way to do this for a section of a map in Chimera? Many thanks, Jason P

2 1

pocket cavity file produced by rdock
by Fabian Glaser 02 Mar '14

02 Mar '14

Hi all, I am trying to upload and examine the cavity file produced by the rbcavity program from rdock, an open source docking program. There are both a binary form and a regular file "RBT FFT GRID" but I am not able to upload or visualize them. Can you please help me to do it? Files are attached. Thanks a lot, Fabian

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Using sym command to generate icosahedral cage
by Yen-Ting Lai 25 Feb '14

25 Feb '14

Hi, I noticed that the sym command can be used to generate icosahedral symmetry, but it requires that the molecule to be oriented in specific ways (222, 2n5, n25, ...), which requires aligning the symmetry axes to the X, Y or Z axes. I am wondering if there is a way to specify the symmetries axes by vectors (instead of aligning them to the three principal axes) and then use sym command to generate the whole icosahedral cage? Yen

2 6

Chimera hardware resources
by Derrick Smith 18 Feb '14

18 Feb '14

Hi Chimera users, I've been working with what are probably some pretty big files (400 MB - 3 GB) for ultramicrotomed sections of holograms. I've trimmed the volume down as well as I can while keeping it large enough to see what we ultimately were aiming for. However, I am running into some hardware resource issues. None of our computers in the lab can handle it, so I've been using my gaming rig at home to do it. I run a server off it also, so have some decent hardware to work with, but I cannot figure out how to reallocate the resources that Chimera seems to default to. I have 64 GB of system RAM available, and after recording 1-2 movies of rotations or a flythrough of clippings etc. Chimera has never used more than 1.5 GB. My graphics card has 4 GB. After filtering and post-processing, before any rotation or video capturing, the vid card has used around 2 GB already. During video capture, depending on if I'm rotating or clipping (clipping uses up a lot more faster), the vid card memory slowly gets eaten up, eventually crashing Chimera altogether. I can usually only get about 800-1000 frames before this happens on a smaller file (400 MB), and usually can't get through a whole 10s, or 250 framed, video on one of the larger files. I have pretty limited experience with this program, so I'm hoping it's a simple settings or otherwise fix I've overlooked. Any suggestions on this? Best, Derrick -- Derrick Smith Drexel University Soft Materials Group Philadelphia PA 19104 dms348(a)drexel.edu http://www.mse.drexel.edu/srg/

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Receptor-Ligand bonding at the LBP
by Graziella Portelli 13 Feb '14

13 Feb '14

To whom it may concern I would like to ask if there is a function where the bonds with which the ligand binds inside the LBP of the receptor would be visualised, or whether one has to search the amino acids involved in binding with the ligand one by one? I thank you in advance for your time Graziella Portelli

3 2

Symmetry-aware segmentation?
by Joel Meyerson 13 Feb '14

13 Feb '14

Is it possible for Chimera to segment with an awareness of symmetry, such that the collection of segments in the asymmetric units are identical? For example, a molecule with C2 symmetry would have two copies of each segment. Also, is it possible to select a segment and then have Chimera further sub-divide that segment into additional segments? Thanks, Joel

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when will NoResidueRotamersError be raised?
by Xiao-Bo Li 13 Feb '14

13 Feb '14

I would like to mutate one residue to another. So far, the only way I found is to use the rotamers of the other residues on the original. I'm using chimera's python script. I would like to know if the NoResidueRotamersError will only be raised for residues that don't have rotamers like GLY. If not, then how can I replace the amino acid residue that I want to mutate? I am using the "getRotamers" function, which returns this error. XBL

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Problem in using BondRot
by amin＠imtech.res.in 13 Feb '14

13 Feb '14

Dear Chimera users, I am trying to write a script to change the phi and psi angle of a peptide. I am trying to adapt the code from http://plato.cgl.ucsf.edu/pipermail/chimera-users/2005-September/000456.html . I am trying to invert the angles so I am multiplying the angles by -1. My code is import chimera from chimera import selection, UserError, BondRot, replyobj opened = chimera.openModels.open('fun.pdb') mol = opened[0] RES_LIST = mol.residues for res in mol.residues: b = str(res.phi) if b != 'None': c = -1*float(b) atomsMap = res.atomsMap N = atomsMap['N'][0] CA = atomsMap['CA'][0] C = atomsMap['C'][0] CAmap = CA.bondsMap phiBond = CAmap[N] psiBond = CAmap[C] phiAnchor = N psiAnchor = CA phi = BondRot(phiBond) phi.setAngle(c, phiAnchor) When I run this script i get the error phi.setAngle(c, phiAnchor) AttributeError: '_molecule.BondRot' object has no attribute 'setAngle' Can someone please help me with this? Warm regards. Amin.

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un-subscribe
by Ted Holman 12 Feb '14

12 Feb '14

hi there i made a mistake and signed up for the email questions on chimera to be copied to me. i tried to un-subscribe but it did not work. can you tell me how to do this? thanks ted ___ Ted Holman, Ph.D. Professor Chemistry and Biochemistry Department 250 PSB, Thimann Receiving University of California, Santa Cruz Santa Cruz, CA 95064 Phone: 831-459-5884 Email: holman(a)ucsc.edu

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vrml lighting
by Dougherty, Matthew T 12 Feb '14

12 Feb '14

I have a multiple vrml models that vary by scale. 1, 10 & 100 I notice the lighting significantly drops off as the scale increases. When I have another model, say PDB, that is in approximate relation (ie, viewable in regards to the volume size similar to the vrml files volumes); the PDB file looks good regardless of size (eg, tRNA or ribosome). I can increase the brightness to compensate (10-20) but it washes out the PDB models when brightness goes beyond 2. is the lighting handled differently between these different types of models? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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superimposing two structures based on a specific selection
by David Martin 10 Feb '14

10 Feb '14

Chimera 1.8 on Windows I have been trying to align (superimpose) models based on a specific conserved region. Unfortunately Chimera doesn't seem to do what the documentation claims it does. I run (example): match #0:5-15@CA,20-30@CA #1: 5-15@CA,20-30@CA and get an RMSD calculation (more on this below), but no movement of the model occurs. I specify 'move true show true' as options. Still no movement but I have a transformation matrix. Unfortunately this is not in a form that can be understood by Transform Coordinates. How do I persuade my structures to superimpose on the specific atoms? The RMSD calculation appears to be broken. If I take the command rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,20-30@CA then I will get a number If I then run rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,21-31@CA I get exactly the same number. In fact, if I specify atom sets of different sizes (as long as it is not the first block) then I continue to get exactly the same number rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,20-35@CA This should fail but doesn't Have I completely misunderstood what Chimera should be doing here? ..d The University of Dundee is a registered Scottish Charity, No: SC015096

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Query on introducing an external protein
by Aditya Padhi 06 Feb '14

06 Feb '14

Dear All, I want to place a protein molecule (appx. 20 kDa in size) into a viral capsid loop region which is about 7 amino acid long. What I want to do is to remove the 5 amino acids out from the loop region and place the 20 kDa protein, so that the loop region can accommodate the 20 kDa protein. I am finding it difficult as the co-ordinates of both the molecules are different. Although, this is not related to MD simulation or associated stuff, it would be grateful if I can get some suggestions. Thanking you, Regards Aditya.

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Query on introducing a protein
by Aditya Padhi 04 Feb '14

04 Feb '14

Dear All, I want to place a protein molecule (appx. 20 kDa in size) into a viral capsid loop region which is about 7 amino acid long. What I want to do is to remove the 5 amino acids out from the loop region and place the 20 kDa protein, so that the loop region can accommodate the 20 kDa protein. I am finding it difficult as the co-ordinates of both the molecules are different. Although, this is not related to MD simulation or associated stuff, it would be grateful if I can get some suggestions. Thanking you, Regards Aditya.

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Question about "Color Zone" and "Render by Attribute"
by Helge Paternoga 04 Feb '14

04 Feb '14

Hello, I have a question regarding the colouring of surfaces and their caps. I am trying to recreate the colouring by hydrophobicity on capped surfaces as shown in (on the right side): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.… So first I've opened the "Render by Attribute" dialog and assigned "kdHydrophobicity". This only coloured the surface and not the surface cap though. I am assuming this is done by "Color Zone"? Indeed this colours the surface cap but I have one problem: The colouring of the surface is different between "Render by Attribute" and "Color Zone" and I don't know why. The differences are small but I would like to know which one is more accurate (intuitively I would say the one from "Render by Attribute"). I've played around with the radius of "Color Zone" but this doesn't achieve the same colouring as "Render by Attribute". So my question is: How can I achieve the same surface colouring by "Color Zone" as in "Render by Attribute"? Does it have something to to with "bondzone" or the hierachy in which the atoms apply their respective colour in "Color Zone"? Thanks for reading! Helge

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Question about opening mrc and PDB files
by Min Woo Sung 03 Feb '14

03 Feb '14

Hi, This is Min Woo Sung from Texas A&M University. I was using Chimera to see EM structure(.mrc file) and wanted to put a PDB file to fit that in EM map. I'm wondering if I can use Chimera to analyze the volume, size or domains of these two files for the purpose of analysis. I saw one PDB file seemed much bigger that EM map when I opened it in Chimera. Do I have to normalize the size of any files? If so, how can I do that? Any suggests would greatly appreciated. Best regard, Min Woo Sung

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Creating output with IDATM naming
by Nikolay Igorovich Rodionov 03 Feb '14

03 Feb '14

Hi, Does anyone know a way to rename all of the atom names in a PDB file to their IDATM types, so that a new PDB file can be generated with the IDATM naming scheme? Best, Nikolay Rodionov

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Zoom problem?
by Damien Larivière 03 Feb '14

03 Feb '14

Dear all, I try to zoom in the scene, to get very close to my model shown here below. I cannot be closer than in the image below, the zooming function is at its maximum. When zooming, I get the error message : /refocus to continue scaling/ I do not know whether it is a bug or something I'm doing wrong. Thanks for your help, Damien

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Need help in Coulombic surface coloring
by Haresh Tukaram More 30 Jan '14

30 Jan '14

Hi, I tried to get the Coulombic surface coloring for one of the protein that I modified by removing certain residue at the C-termini and then mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine using Swisssidechin option. I am getting this error which I am not able to understand. Disabled GPU programs because a graphics driver bug was encountered while compiling a vertex shader. #0, chain A: COMP #0, chain B: COMP #0, chain C: COMP #0, chain D: COMP #0, chain E: COMP C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2 22 connected surface components Total solvent excluded surface area = 10393.6 component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059, 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549, 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319, 26.9429 Total solvent accessible surface area = 10372 component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165, 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737, 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394, 0.0674059, 0.0311705 No SEQRES records for combination (#-2147483648.-2147483648) chain A; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain B; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain C; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain D; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain E; guessing terminii instead Chain-initial residues that are actual N terminii: #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B, #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D, #-2147483648.-2147483648 MET 27.E Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B, #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D, #-2147483648.-2147483648 TFLE 67.E Chain-final residues that are not actual C terminii: 424 hydrogen bonds Hydrogens added Charge model: AMBER ff12SB Assigning partial charges to residue TFLE+TFLE (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (TFLE+TFLE) Cannot automatically determine charges for residue TFLE+TFLE; Run AddCharge tool manually to add charges and then rerun ESP Can someone please tell me a step by step procedure to make this work. Thanks & Regards, Haresh

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Re: [Chimera-users] Coloring map by curvature
by Tom Goddard 29 Jan '14

29 Jan '14

Hi Joel, I don't think surface curvature will be helpful understand the differences between two EM maps. But I was curious what it would look like. So here's a Python script and an image on a simulated map at 15 Angstroms. You use the script by opening your map, selecting the surface (ctrl-click on it), then open the curvature.py script (menu File / Open…). Here's a description of the method it uses from the comments at the top of the curvature.py file. # Color selected surface pieces by mean curvature. # # Gray at the average curvature value over the surface, and blue and red # at +/- 3 standard deviations of curvature values across the surface. # # The curvature is estimated from the vertices and normals of the triangulated # surface in simple way which will show artifacts from non-isotropic meshes. # For each triangle edge it computes the normal vector rotation from one vertex # to the other divided by the edge length. The vertex mean curvature is the # mean of the curvatures computed for each edge. # And the steps to make the example image open 1grl molmap #0 15 grid 2 model #1 select #1 open ~/Desktop/curvature.py Tom On Jan 29, 2014, at 9:40 AM, Joel Meyerson wrote: > Hi Darrell, > Thanks for the tip! I hadn't considered mesh lab but that link you sent looks promising. I'll also wait to see if Tom has any further suggestions. > Joel > > > On Wed, Jan 29, 2014 at 11:44 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: > Hi Joel, > > I love Chimera and use it all the time. However, a quick-and-dirty solution to your problem might be to try Meshlab. It is kind of buggy software, but can be very useful. Here's a tutorial/blog entry that I found in a quick search. At the very least, it describes what I think Tom was communicating about enhancing surface shading: > http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-a… > > FWIW, > 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 > > > 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. > > From: <Meyerson>, "Joel [F] (NIH/NCI)" > Date: Tuesday, January 28, 2014 9:08 PM > To: Tom Goddard > Cc: "chimera-users(a)cgl.ucsf.edu List" <chimera-users(a)cgl.ucsf.edu> > > Subject: Re: [Chimera-users] Coloring map by curvature > > Hi Tom, > I have cryo-EM maps for two conformations of a protein, both in the 15 Angstrom resolution range. The conformations are visibly different, but I am also interested in seeing where they differ in terms of their surface curvature, as it could have bearing on how I interpret the conformations. If there's any other info I can provide just let me know. > Thanks! > Joel > > > On Tue, Jan 28, 2014 at 7:36 PM, Tom Goddard wrote: > Hi Joel, > > No, Chimera does not compute surface curvature. It would not be too hard to make a Python script that computed it and used it to color a surface. The main trouble is defining numerically the curvature for a triangulated surface at each vertex. Why are you interested in this? Is the idea to simulate ambient occlusion lighting where surface cavities are dark and projections are brighter? Is the idea to try it on EM maps or molecular surfaces? > > Tom > > > On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote: > > > Hi, > > Is it possible to color a map based on surface curvature? > > Thanks, > > Joel > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > >

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