- Chimera-users - RBVI Mailing Lists

Flickering graphics
by Thomas Goddard 22 Dec '06

22 Dec '06

Hi Murali, What kind of flickering do you see when moving maps in Chimera? Does the surface appear shattered? One nvidia graphics driver bug I have seen causes the surface to appear broken into many triangles instead of smooth while it is moved. Or is it tearing that you see? That is when the top half of the screen momentarily shows one position for the map but the bottom shows a different one. That happens because you are moving the model and the redraw is not synchronized to the vertical refresh of the display. That is a graphics driver setting problem. Or does flicker mean it appears like every other frame is black? Every possibility I can think of points to a graphics driver problem, not a Chimera problem. You can check on Linux what graphics driver you are using with the glxinfo command: % glxinfo ... OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Quadro4 500 GoGL/AGP/SSE2 OpenGL version string: 1.5.2 NVIDIA 66.29 ... The OpenGL renderer and version lines tell you the driver. If it says "Mesa" this means you have no driver installed and it is using software rendering (no hardware acceleration). Usually a new Linux system does not have a graphics driver installed by default so you have to get the driver from the NVidia web site. http://www.nvidia.com/content/drivers/drivers.asp The latest Nvidia GeForce driver version is 9746. The first step to try to fix your problem is update to the newest driver. Tom > Date: Fri, 22 Dec 2006 09:42:43 -0600 > From: "Murali Ayaluru" <mayaluru(a)gmail.com> > To: goddard(a)cgl.ucsf.edu > Subject: flickerings in model > > Hi, > > Greetings! > > I am using Chimera (chimera-1.2304-linux.exe) in Linux (FC-6) environment. > Basically I use this > for visualizing the structures generated from EM. While moving the model > (either vertical or horizontal) and also while rendering the volumes, I saw > lot of flickering in the model. Is there some parameter I have to change > to fix this problem? The graphic card we use is nVidia GeForce 7300 LE. I > don't have much experience in linux OS. Any suggestions to fix the problem > will be highly appreciated. > > Thanks and have a nice day. > > Regards, > Murali

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Benchmark results
by Daniil Zaitsev 19 Dec '06

19 Dec '06

hi - here is benchmark result for new version of Chimera. Original benchmark progress log file is attached. Graphics NVidia GeForce Go 7200 Processor Intel Core Duo T2050 Clock (MHz) 533 OS Type Windows Surface 990 Mesh 368 Contour 148 Solid 173 Recolor 87 Notes Laptop Test Date 12/06 Chimera Version 2304 Machine HP Pavilion dv2000t Graphics Memory (Mb) 128 Main Memory (Mb) 1024 OS Version XP Home Driver Version 8.4.6.4

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compressed versus gzipped Re: Read compressed PDB files -question, suggestion
by Moo Cow 12 Dec '06

12 Dec '06

A thousand pardons. You are right. I phrased the question wrongly. Chimera does open gzip'd files ( xx.gz). It does not open compress'd files (xx.Z). > You can also open gzipped files with Chimera's "open" command or as > an argument as you start Chimera. [...] > > You can use the Chimera File / Open... dialog to directly open a gzip > > PDB file. This was added to Chimera about one year ago. It does not work Why, you may ask, would anyone use compress these days ? If you mirror or rsync the protein data bank, they are still distributing files that have been squashed with compress and have a ".Z" extension. gunzip will happily eat and uncompress these files. I do not know how chimera handles compressed files. If it reads from a pipe, it might be nice to persuade it to feed .Z files to gunzip. I think it might be more difficult if chimera uses the python/zlib interface. Many thanks -- Search for products and services at: http://search.mail.com

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SDF format
by Randy Heiland 12 Dec '06

12 Dec '06

Just wanted to ask about Chimera's support for reading in SDF formatted files, e.g. from PubChem. It seems not to be one of the supported formats. Obviously we can use a converter to get pdb format, but thought I'd ask the experts. Thanks, Randy

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Transparent Ribbon
by Anna Feldman-Salit 12 Dec '06

12 Dec '06

Dear All, From some reason I cannot find the option of making ribbon representation transparent. Can you please give me a hint? Thanks a lot in advance, Anna

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saving with angles
by Gabor Papai 12 Dec '06

12 Dec '06

Dear everybody, Is there a way in Chimera to save density maps when I rotate them with the modified angles? In practice, I use the 'fit map in map' to align two maps in respect to each other and I would like to save them for further analysis with different softwares. Therefore I would like to conserve their position (shift and rotation). Thanks in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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Delphi Controller
by sette＠uniroma2.it 11 Dec '06

11 Dec '06

Dear all, I have a simple question: does Delphi controller works under unix only or it is possible to work with it under Linux and/or Windows XP? Thanks a lot, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Read compressed PDB files -question, suggestion
by Moo Cow 08 Dec '06

08 Dec '06

We store the PDB locally, but compressed. Can one persuade chimera to read coordinates from a pipe ? Maybe this could be done at the python level. It might also not be too hard to use the python binding to the zlib library, but I would not know how to do this. I imagine the interest (or not) would not be limited to reading PDB files. many thanks for any suggestions. -- Search for products and services at: http://search.mail.com

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Apply the symmetry to the fitted models in map
by Hong-Wei Wang 06 Dec '06

06 Dec '06

Hi, Tom I remember you were showing docking a model into map with high symmetry (you showed the actomyosin filament example). I am wondering how you generate the symmetry in the docking and if the symmetry information is necessary for the correct fitting. Thanks a lot! Hongwei ----------------------------------- Hongwei Wang, Ph D MS 20A-355, LSD, LBNL 1 Cyclotron Rd, Berkeley, CA 94720 510-642-2222 (O) 510-642-8806 (FAX) hwwang(a)lbl.gov

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volume viewer issue
by Matthew Shawkey 06 Dec '06

06 Dec '06

Hi, I am using chimera to visualize a stack of EM serial sections. I can load them into Chimera (as MRC file), but when I try to view the stack in the volume viewer w the "solids" option all I see is a white square.. w the mesh and surface options the stack shows up as a grainy image on which it's difficult to see any depth.. any suggestions? THanks, Matt

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