November 2010 - Chimera-users - RBVI Mailing Lists

reset/stereo
by Dougherty, Matthew T 29 Nov '10

29 Nov '10

I had a couple questions about using the reset command. Let's say I have two keyframes (e.g., kf0,kf1) such that the stereo parameters are different between the two. 1) If I do a "savepos kf0" are the stereo parameters saved as part of the keyframe? 2) If I start at kf0 and do a "reset kf1 100", should the stereo parameters be interpolated across the 100 frames? thanks, Matt

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3D dashed lines
by M Sundaramoorthy 29 Nov '10

29 Nov '10

I like to show pseudobonds (H-bonds, metal coordinations and distances) as solid dotted or dashed lines. To draw dashed/dotted line I can choose dashed line style in the Pseduobond attributes panel. But it works only with bond style 'wire' not with 'stick'. It can essentially draws flat lines. How do I show 3D dashed/dotted lines? Some images in the tutorial do have such lines represented as dotted (spheres) lines. Another problem I have is that the Side View panel shows the image but does not show the eye (the small square) and the clipping planes (vertical lines). I am using Chimera 1.5rc in Windows Vista. Thanks Sundar

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Exporting .stl
by Dennis Kolva 25 Nov '10

25 Nov '10

I have been using Chimera to export .stl files of proteins and RNA for 3D printing. The surface models print OK, but sticks or ribbons choke the printer. I looked close at the output meshes, and they have many extra surfaces which should be removed to make "legal" .stl format. Is that portion of the code open source? I'd like to take a closer look and see if it's possible to fix. It would be much easier to rectify the bad surfaces upon creation, rather than trying to remove them by post-processing. Thanks, Dennis Kolva Cornell U.

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PDB with C alpha carbons only
by Sujata 23 Nov '10

23 Nov '10

Hi, I have a PDB file with C-alpha carbons only. I want to know if Chimera can add backbone atoms and sidechains (the PDB has the names of the residues). Thanks, Sujata

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Re: [Chimera-users] Fwd: Re: 3D stereo
by Nadir T. Mrabet 22 Nov '10

22 Nov '10

Hi Greg, Both DepthQ and Christie (made in fact by the same manufacturer. http://www.depthq.com/projector.html; http://www.depthq.com/christie.html) are, as expected, sold in France by a unique firm. They say that DepthQ HDs3D-1 ($2,995) has no capability for 3D for a conference room with 30-50 people, and that my only option is Christie (> $65,000!). Your earlier mail states that DepthQ can go along with a 3-meter size screen, suggesting it could accommodate an audience of 30-50 people. Can you, please, comment on all these issues and eventually let me know if I can go along with DepthQ DLP? Many thanks in advance. Best, Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet<at> medecine.uhp-nancy.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. On 28/09/2010 12:59, Greg Couch wrote: > > Subject: Re: [Chimera-users] 3D stereo > Date: Tue, 28 Sep 2010 12:59:13 -0700 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Nadir.Mrabet(a)medecine.uhp-nancy.fr > CC: Chimera-users(a)cgl.ucsf.edu > > > > On 07/21/2010 07:24 AM, Nadir T. Mrabet wrote: > > Hi, > > > > This is for teaching purposes so that students can "walk" though 3D structures. Would it be possible to use Chimera via a 3D stereo beamer to project display on a very large screen and watch the selected structure in 3D by means of shutter glasses? If this is so, what kind of equipment would you recommend? > > > > Many thanks, > > > > Nadir > > So there were some developments at SIGGRAPH, but nothing that would > change the previous recommendations made in the chimera-users mailing list. > > To summarize, for a large group of people, you want a setup similar to > what is done for 3D movies in a movie theater, which is to use left-hand > and right-hand circularly polarized light for the left-eye and right-eye > images. There are three parts to the setup: (1) projecting the stereo > images, (2) reflecting the images, (3) receiving the images at the eyes. > > 1. For projecting the stereo images with chimera, you need a > workstation-class graphics card, either an AMD FirePro (or ATI FireGL) > or a NVIDIA Quadro (or Quadro FX, not Quadro NVS), and either (a) two > projectors with passive polarizers, or (b) a single projector with an > active polarizers. The single projector method is much simpler to > maintain because you don't have to keep aligning the two projectors, but > may cost more because the projector has to be able to display at 120Hz > (and there's the cost of the active polarizer). The relative costs of > the two options vary. Active polarizers are available from DepthQ, > http://www.depthq.com/, and RealD, > http://www.reald.com/Content/professional.aspx. DepthQ also sells a 3D > projector that can display 3 meter wide images, and has European > distributers, so that might be the best choice. If you want a larger > image, you'll need a Christie Mirage or a Barco projector. > > 2. To reflect the stereo images, you need a screen that doesn't change > the polarization of the light. There are lots of choices. Google for > "3D projection screen" to see what's available. What screen you want > depends on the layout of the room that the stereo projection will be > in. Narrow rooms can use screens with a smaller viewing cone and higher > gain. I've heard good things about Stewart Filmscreen, but get > recommendations from whoever you buy your projector too. > > 3. Last part of making sure each eye only receives the image it is > supposed to is for the person to wear circularly polarized glasses. > Google for "polarized 3d glasses" to see what's available. I'd avoid > the disposable paper ones. I like the RealD glasses that the movie > theaters use. Perhaps a theater would sell some to you. The glasses > from Zalman displays work too. > > Bon chance, > > Greg >

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adding density maps
by Anindito Sen 22 Nov '10

22 Nov '10

Dear All I was wondering if there is an option to add multiple density maps of the same box and voxel sizes in Chimera. Thanks Andy Dr. Anindito Sen (Ph.D)

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Measure volume of a cavity encased inside a cryo-EM density
by sudheer molugu 19 Nov '10

19 Nov '10

Hi, I was just wondering if chimera can calculate the volume of a central cavity encased inside the cryo-EM density. Thanjk you, Kumar

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Chimera SASA algorithm
by Devin McBride 17 Nov '10

17 Nov '10

Hello, I have been using UCSF Chimera for a few years. I am currently reviewing the SASA algorithms by various molecular modeling software. I was wondering what the error associated with a given SASA calculation is? The algorithm has an error in the calculated SASA, but I was not able to find out what the error is. Thank you very much for your time and help. -- Devin McBride Ph.D. Candidate Department of Bioengineering Bourns Hall A130 University of California, Riverside Phone: (951) 742-3541 Email: dmcbr001(a)student.ucr.edu

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visualization code optimized using GPU shaders ?
by Mathieu Chavent 16 Nov '10

16 Nov '10

Dear Chimera developers, I try to have a brief overview of molecular programs that can use programmable capabilities of new graphic hardwares (i.e. use of shaders): So, I would like to know if Chimera program have dedicated code that use such shaders to visualize fastly surfaces or to add particular lighting effects.. Thank you in advance. Matthieu Chavent.

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About GPU accelerating on Chimera
by Allan Hou 16 Nov '10

16 Nov '10

Hi Sir, I would like to get help from you to confirm whether Chimera use GPU accelerating function. I have a customer and they are using Chimera: * Customer: Institute of Biophysics of China * Platform: Dell 5500 workstation, Windows VISTA 64bit OS, FX4800 , Quadro driver version : 259.81, * Application: UCSF Chimera 1.5 for protein molecule analysis * Status: Chimera for 64bit OS , the graphic 3D performance would be 5 times fast than Chimera for 32bit OS in VISTA64 * Need to check: Whether Chimera using CUDA/GPU accelerating function Best Regards, Allan Hou(侯宇涛） Enterprise Account Sales Manager Nvidia China 0086-13801005536 ----------------------------------------------------------------------------------- This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. -----------------------------------------------------------------------------------

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Chimera-users November 2010