- Chimera-users - RBVI Mailing Lists

selection color
by George Tzotzos 26 Mar '14

26 Mar '14

Hi everybody, I’ve conducted Principal Component Analysis on a trajectory and generated an ensemble of structures (see attachment, pc2.pdb). There should be a way of coloring (occupancy?) the most mobile regions of the protein (e.g. residues 67 - 72). I haven’t found a way to do this. Any help would be much appreciated. Best regards George

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stereo3D
by Dougherty, Matthew T 26 Mar '14

26 Mar '14

I have a toshiba qosmio x875-7390 S3D laptop, which is based on the NVidia NVision 3D. Toshiba structured the device to be user unfriendly, limiting stereo3D for bluray and youtube 3d via adobe flash. coming across a pymol S3D post I see there is a workaround, for a different Toshiba model. http://nanonan.wordpress.com/2012/03/28/pymol-and-coot-3d-stereo-on-qosmio-… http://coxcoppes.nl/3DScreenActivator/index.php?pagina=1 Any comments about chimera using S3D on NVidia NVision 3D? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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(no subject)
by Francesco Pietra 23 Mar '14

23 Mar '14

Hello: About stereo drawings with chimera (GNU Linux), I received from the editorial staff: All stereoview illustrations have been drawn in the cross-eye mode, i.e. the > picture for the right eye is on the left and vice versa. > Has this been chosen deliberately? In our opinion, the parallel-eye mode > seems to be used more often. > Please let us know whether we should switch the figures (you would not need > to send new ones) or not. They did the job of transformation to parallel-eye. Next time, I would like to be able to do that myself, while I don't see the parallel-eye mode in chimera. Which is the equivalent? thanks francesco pietra

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Detection of Internal water along MD trajectory
by James Starlight 20 Mar '14

20 Mar '14

Dear Chimera users! I've performed md simulation of water soluble protein having water-assessable channel in its interior. I'd like to perform analysis of average number of water molecules detected within the protein interior during MD trajectory with the possible visualization of such internal water binding sites. Does SASA calculation which I've seen in vmd could provide me with additional insights? I'd be thankful if you provide me with some Chimera tools suitable for such task. Many thanks for help, James

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Chimera Sequence alignment window
by meginir urestal 20 Mar '14

20 Mar '14

Hi, I was wondering if there was a way of printing the contents of the chimera alignment window. If not, could anyone suggest something for printing saved aligned fasta sequences. Thanks

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Morph conformation - conformation collapsing
by Helge.Paternoga＠bzh.uni-heidelberg.de 18 Mar '14

18 Mar '14

Hello, I'm trying to morph two structures which have two chains each. The problem is that if I just add the two confirmations one chain will turn the wrong way, because it is taking the shortest distance to the final position. What i did now is I used this initial morphing to extract 4 frames of the movement of the other chain and inserted the movement of the smaller chain in each of these structures by hand (so the movement is in the right direction and happening at the same time as the other chain). But when I now add these 4 structures in my morph confirmation list like this: Start confirmation frame 1 frame 2 frame 3 frame 4 End confirmation It nicely starts moving in the right way but then at a transition to a new frame the whole structre collapses, bonds get distorted, it somehow shrinks and then extends again later to end up at the final confirmation... I think this is independent of which frame i use (I tried to simplify it by using only 2 intermediates) Do you have any idea what is causing this collapse? The initial confirmation has the same number of chains as the end confirmation (with the same names) but they have a different number of atoms (which i don't quite understand because they are the same macromolecules...) Could this be part of the problem? best regards, Helge

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Recording movie with simultaneous map morph and PDB morph conformation
by Joel Meyerson 17 Mar '14

17 Mar '14

Hi, Is it possible to record a movie that shows both an MRC map morph and PDB conformation morph happening simultaneously? Joel

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residue number in Gromacs tpr file
by Mario Dejung 17 Mar '14

17 Mar '14

Hi all, I am experimenting with Gromacs a little bit and try to open the tpr file and the corresponding trajectory in chimera. Works fine, but the numbering is completely wrong. The residues get numbered continuous and not starting at 1 for the next chain. Not sure if the problem is in the tpr file or in chimera. I have 4 chains in my pdb file and all have a chain identifier, O P g and h and they are separated by TER I have also 4 .itp files with names like “topol_Protein_chain_O.itp” My topol.top file say 4 molecules [ molecules ] ; Compound #mols Protein_chain_O 1 Protein_chain_P 1 Protein_chain_g 1 Protein_chain_h 1 and ; Include chain topologies #include "topol_Protein_chain_O.itp" #include "topol_Protein_chain_P.itp" #include "topol_Protein_chain_g.itp" #include “topol_Protein_chain_h.itp" I create my tpr file with grompp Has anybody experience with this kind of issue? Kind regards Mario

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Chimera and XP?
by Boaz Shaanan 13 Mar '14

13 Mar '14

Hi, For some reason, I couldn't get Chimera (1.8.1 and the 12/3 daily build) to work today on my laptop running XP (32bit). It gets stuck in 'initializing graphics'. See attached screen shot of run with --debug. Chimera worked for years on this machine. Other programs work fine (spdbv, Coot, etc.). I can't imagine it has to do with the imminent downfall of XP support, or maybe it does? Please advise. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Wednesday, March 12, 2014 9:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 131, Issue 13 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. match-align using just selected protein areas ? (Marek Maly) 2. Re: match-align using just selected protein areas ? (Elaine Meng) 3. Re: surface failures (Elaine Meng) 4. Re: match-align using just selected protein areas ? (Marek Maly) ---------------------------------------------------------------------- Message: 1 Date: Wed, 12 Mar 2014 02:53:47 +0100 From: "Marek Maly" <marek.maly(a)ujep.cz> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] match-align using just selected protein areas ? Message-ID: <op.xck57xhvlc8gdf(a)pocitadlon.ujep.cz> Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes Hello, I would like to know if it is possible in Chimera align two proteins let say protein A and protein B, but just using selected subsequences A_sel, B_sel (i.e. just the selected subsequences are going to be optimally matched and the rest of both proteins is not involved in the matching process/calculation) ? Thank you in advance ! Best wishes, Marek -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ ------------------------------ Message: 2 Date: Wed, 12 Mar 2014 09:35:39 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: "Marek Maly" <marek.maly(a)ujep.cz> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] match-align using just selected protein areas ? Message-ID: <67EFA59C-7032-4F2A-8517-6D32E11C4F2D(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Marek, Yes, if you mean MatchMaker (Match->Align does not align the structures, it just makes a sequence alignment from a structural alignment you already made). In the MatchMaker GUI, there is a "Further restrict matching to current selection" setting: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> In the matchmaker (mmaker) command, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> ... it is similar but you instead specify the residues directly instead of selecting them: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict> 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 11, 2014, at 6:53 PM, Marek Maly wrote: > Hello, > I would like to know if it is possible in Chimera > align two proteins let say protein A and protein B, > but just using selected subsequences A_sel, B_sel > (i.e. just the selected subsequences are going to be > optimally matched and the rest of both proteins is not involved > in the matching process/calculation) ? > Thank you in advance ! > Best wishes, > Marek ------------------------------ Message: 3 Date: Wed, 12 Mar 2014 09:51:04 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Julian Marzi <julian.marzi(a)googlemail.com> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] surface failures Message-ID: <91C53A76-7F10-4123-9752-0AE5F5C58689(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii On Mar 12, 2014, at 6:46 AM, Julian Marzi wrote: > Dear Eric, > I tryed the command surfcat c1 and surfcat c1 :.1 & ~:ohx, but this will also not work on my mac... The mac show for short time an activity, but nothing happens. The comand from Elaine molmap :.1&~:ohx 5 worked and it looks great! Is there also a possibility to select a part of the sequence in the "surface" (molmap) presentation to show it in an other color? I select one part on the 25S-rRNa in green, but the molmap view covers it in grey and if I make a higher transparency, the selected part will be seen. But it would be better, if the selected part is colored in the molmap view. This would allow the marked spot directly recognize without transparency. If there is an answer for my question, please let it me know. If not, is not bad, you two have helped me incredibly much. > Thank you so much > Regards > Julian Hi Julian, The "molmap" surface can be colored to match atoms with the Color Zone tool. The atoms can be hidden, it is just a step to the surface coloring that you want. After you color some atoms (for example, some part of the RNA that you selected) you can also color the part of the surface that is near the currently selected atoms with Color Zone (in menu under Tools... Depiction). Color Zone is mentioned along with molmap in #3 in the surface workarounds page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzo…> Also, you could color the molmap surface any overall color you want first, it doesn't have to be the default grayish color. You could just click the color square on the Volume Viewer tool (that appears when you create the molmap surface) and then use the Color Editor, or you can select the surface directly in the main window and use the Actions... Color menu. I hope this helps! P.S. please send chimera questions to the chimera-users address instead of our individual addresses (to allow others to see the Q & A) - thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco ------------------------------ Message: 4 Date: Wed, 12 Mar 2014 19:44:27 +0100 From: "Marek Maly" <marek.maly(a)ujep.cz> To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] match-align using just selected protein areas ? Message-ID: <op.xcmg0dxylc8gdf(a)pocitadlon.ujep.cz> Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes Dear Elaine, thank you very much for your help ! Best wishes, Marek Dne Wed, 12 Mar 2014 17:35:39 +0100 Elaine Meng <meng(a)cgl.ucsf.edu> napsal/-a: > Hi Marek, > Yes, if you mean MatchMaker (Match->Align does not align the structures, > it just makes a sequence alignment from a structural alignment you > already made). > > In the MatchMaker GUI, there is a "Further restrict matching to current > selection" setting: > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> > > In the matchmaker (mmaker) command, > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> > ... it is similar but you instead specify the residues directly instead > of selecting them: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict> > > 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 11, 2014, at 6:53 PM, Marek Maly wrote: > >> Hello, >> I would like to know if it is possible in Chimera >> align two proteins let say protein A and protein B, >> but just using selected subsequences A_sel, B_sel >> (i.e. just the selected subsequences are going to be >> optimally matched and the rest of both proteins is not involved >> in the matching process/calculation) ? >> Thank you in advance ! >> Best wishes, >> Marek > > > __________ Informace od ESET NOD32 Antivirus, verze databaze 9532 > (20140312) __________ > > Tuto zpravu proveril ESET NOD32 Antivirus. > > http://www.eset.cz > > > -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ ------------------------------ _______________________________________________ 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 13 **********************************************

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'Old-style' silhouette edges?
by Thomas Mitterfellner 13 Mar '14

13 Mar '14

Hello! It seems that somewhere between 1.6.2 and 1.7, the way silhouette edges are drawn has changed. Most of the silhouette edges are now drawn in white regardless of the color I set (presumably due to some smart algorithm?). In my opinion, the old way gave a much clearer appearance of the molecule on different backgrounds and it gave it a 'cartoonish' flavor which made it look quite distinguished from the images other software produces and I really loved that. So my question is: is there any way to get back the 'old-style' (pre 1.7) silhouette edges in 1.7+ releases? Kind regards, Thomas

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editing selected dihedral angles
by Francesco Pietra 13 Mar '14

13 Mar '14

Hello: I would appreciate receiving instructions on changing selected dihedral angles in a peptide. Imagine that the initial and final stretches are alpha-helices, while in the middle, dihedral angles are such that two alpha-helix coiled portions make an angle different from 180 degrees. In all that, all dihedrals in the alpha-helix portions should not be modified. Thanks francesco pietra

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anti aliasing
by George Tzotzos 12 Mar '14

12 Mar '14

Hi everybody, I’m trying to produce images of a protein for publication. However, using the publication presets, I get jagged edges in ribbons/helices. Is there a way to set up the anti aliasing. Thank you in advance for any suggestions Regards George

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match-align using just selected protein areas ?
by Marek Maly 12 Mar '14

12 Mar '14

Hello, I would like to know if it is possible in Chimera align two proteins let say protein A and protein B, but just using selected subsequences A_sel, B_sel (i.e. just the selected subsequences are going to be optimally matched and the rest of both proteins is not involved in the matching process/calculation) ? Thank you in advance ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Re: [Chimera-users] surface failures
by Elaine Meng 12 Mar '14

12 Mar '14

On Mar 12, 2014, at 6:46 AM, Julian Marzi wrote: > Dear Eric, > I tryed the command surfcat c1 and surfcat c1 :.1 & ~:ohx, but this will also not work on my mac... The mac show for short time an activity, but nothing happens. The comand from Elaine molmap :.1&~:ohx 5 worked and it looks great! Is there also a possibility to select a part of the sequence in the "surface" (molmap) presentation to show it in an other color? I select one part on the 25S-rRNa in green, but the molmap view covers it in grey and if I make a higher transparency, the selected part will be seen. But it would be better, if the selected part is colored in the molmap view. This would allow the marked spot directly recognize without transparency. If there is an answer for my question, please let it me know. If not, is not bad, you two have helped me incredibly much. > Thank you so much > Regards > Julian Hi Julian, The "molmap" surface can be colored to match atoms with the Color Zone tool. The atoms can be hidden, it is just a step to the surface coloring that you want. After you color some atoms (for example, some part of the RNA that you selected) you can also color the part of the surface that is near the currently selected atoms with Color Zone (in menu under Tools... Depiction). Color Zone is mentioned along with molmap in #3 in the surface workarounds page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzo…> Also, you could color the molmap surface any overall color you want first, it doesn't have to be the default grayish color. You could just click the color square on the Volume Viewer tool (that appears when you create the molmap surface) and then use the Color Editor, or you can select the surface directly in the main window and use the Actions... Color menu. I hope this helps! P.S. please send chimera questions to the chimera-users address instead of our individual addresses (to allow others to see the Q & A) - thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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surface failures
by Julian Marzi 11 Mar '14

11 Mar '14

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

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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

2 1

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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