January 2008 - Chimera-users - RBVI Mailing Lists

graphics card question (survey?)
by William Jeffrey Triffo 31 Jan '08

31 Jan '08

hello, anyone out there using a Radeon HD 2600 XT or GeForce 8800 GT? Just wanted to know if there are any driver issues out there that are known - these are the two 'lower-end' options on the current Mac Pro line, and I am evaluating that as a potential purchase (so technically, my question may only be relevant if you are also using a Mac machine). likewise, if you have a current-generation Mac (Tiger/10.4 or Leopard/10.5) and have bought a third-party card that you have had success with, I am all ears. best, -Jeff -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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fourier transforms
by Matt Shawkey 31 Jan '08

31 Jan '08

Hi, I'm doing fourier transforms of 3d volumes and noticed that they are computed in Chimera using only a small portion of the actual data available (e.g. 128 ^3 pixels rather than the 512^3 pixels in the volume). Is there a way to do a fourier transform using all of the available data? THanks, Matt

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Surface color
by James Fethiere 31 Jan '08

31 Jan '08

Hi, I'm using the volume path tracer and color zone to highlight regions of a map. I would like to display a model within this region but it is not visible when I color the region with color zone. How can I make this zone transparent but still a different color that the rest of the map? Thanks James

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Re: [Chimera-users] mac pro theoretical question
by Tom Goddard 30 Jan '08

30 Jan '08

Hi Jeff, I don't know much about any of the current Apple graphics cards (Radeon HD 2600 XT 256Mb, Nvidia GeForce 8800 GT 512Mb, Nvidia Quadro FX 5600 1.5Gb). My first concern would be whether bugs in the drivers for these cards are going to cause trouble in Chimera. We have a web page that lists problems with graphics drivers observed using Chimera: http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html#cards There was a recently reported problem (squashed atom spheres) with GeForce 8800 GTX (not GT) on Windows. The Apple driver may be much different. The Quadro FX 4500 which was Apple's high-end offering before the 5600 crashed with solid volume rendering. Don't know if the current 5600 would have the same problem -- but there is a fair chance it does. Chimera uses many different OpenGL calls and I'd guess 1 in 10 drivers exhibit bugs of varying severity when using Chimera. Some of Chimera performance is related to graphics card speed and memory, and some is related to CPU speed and memory. When the displayed models rotate slowly that is the graphics card except if you are using transparent volume surfaces or meshes which are sorted by depth on the CPU for every new view angle. Everything else is the CPU, main memory, memory cache performance, and hard-drive speed. Solid style volume rendering makes a lot of textures which usually will be stored in graphics card memory. More graphics card memory could make larger volume rotate faster because they fit on the card. 256^3 volumes (16 million voxels, 4 bytes per voxel) typically rotate at 10 frames per second with graphics memory sizes 128 Mb and up. Textures have to have power of 2 sizes so just knowing that can get you better performance if you trim your 550x550x100 region to 512x512x100 you'll get a factor of 4 speed-up. I don't know if a single application using one display can use more than one graphics card in Apple's multicard options. Chimera has no special code to do that. For large volume data, hard-drive speed, main memory size, and CPU speed are likely to be noticable factors in Chimera performance, each of about equal importance to graphics card speed. Tom > hi Tom, > > if you were considering a Mac Pro at some point in the future, what > graphics card would you pick when thinking of chimera (if you don't > mind peeking at some point at the list at > http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore.woa/9354001/wo/… > > > are rendering bottlenecks in chimera largely a processor-limited thing > (and thus one of the 'lower end' cards listed would be fine), or > something that benefits dramatically from spending $2000 on a graphics > card (I am not in that kind of market, just wondering what kind of > decision you would make if evaluating that platform) > > best, > > -Jeff > > >

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average vs ensemble
by Rachel Scherer 29 Jan '08

29 Jan '08

Given that chimera doesn't calculate average NMR structures, this query may be outside the groups interests, but can anyone suggest what the appropriate protocol is when making aa-substitutions into an NMR structure: should an "average" be calculated (by averaging the atom coordinates across all the models in a PDB file that predates inclusion of the average into the database entry) or, should one use a representative from a cluster generated with "ensemble cluster" be chosen? Or an average of the representatives of the clusters? Or, the cluster representative that best matches the calculated average? -- Rachel Scherer rachel(a)bio.umass.edu Biology Department (413)545-2825 vox UMASS Amherst (413)545-3243 fax

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coordinates
by hsosa＠aecom.yu.edu 25 Jan '08

25 Jan '08

Hi, I am trying to rotate a molecule around a 3D density map. I had already saved the coordinates of the molecule relative to the map. However if I rotate the pdb file (creating a new pdb file with the rotated molecule) by rotating the coordinates around the origin (0,0,0) the new molecule is rotated around a a center that does not coincide with the center of the map. So I am confused about what are the relative positions of the origin for the map and pdb file. If I have an atom with pdb coordinates 0,0,0 should this atom appear at the center of the density map ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Re: [Chimera-users] Save a transformed density map
by Thomas Goddard 25 Jan '08

25 Jan '08

Hi Keren, Chimera has a resampling capability for extracting regions of a map that aren't aligned with the axes. It doesn't work well in the case you want. So I've made a Chimera command that will do what you want. If your the map you wish to save in the new orientation has id number 0 (listed next to the name of the map in volume dialog), and the map you fit into has id 1 you would use the command: vop #0 resample onGrid #1 The vop stands for "volume operation". (Use menu Favorites / Command Line to type commands.) This will create the new map which will appear in the volume dialog and can be saved with the volume dialog File / Save map as... (or using a command like "volume #2 save /tmp/newmap.mrc"). The vop command with the resample operation will be in tonight's builds of Chimera (assuming they succeed). http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom Keren Lasker wrote: > hey Tom, > > I need to save the transformed map for other calculations. Is there a > resampling option in chimera? if not I guess that I can use the output > transformation matrix generated by fit map2map - right? > > thanks, > Keren. > On Jan 24, 2008, at 3:27 PM, Thomas Goddard wrote: > >> Hi Keren, >> >> You can save the Chimera session to preserve the orientation of one >> map fit into another. >> >> If you want to write a new map so that when it is loaded in Chimera >> and other software it will be at the correct place in the map it was >> fit into that is harder. The problem is that none of the map file >> formats provide for a positioning transformation in the header. So it >> would be necessary to resample the map that you fit on the grid of the >> map you fit into. Resampling interpolates data values and can degrade >> map quality. Do you want to do that? >> >> Tom >

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volume visualization
by Enrico Malito 25 Jan '08

25 Jan '08

Hello, I am trying to visualize a map as Volume (ccp4 format map calculated with VOIDOO in NEWZD then converted with MAPMAN) and somehow the map in chimera results shifted with respect to the corresponding pdb model (in a completely different place). If I open same pdb and map file in other visualization programs they are actual in the right position (map into the cavity of the enzyme). I'm opening the map from the Volume Viewer-->File-->Open map Am I doing something wrong? Thanks, EM -- Enrico Malito Ben-May Department for Cancer Research Center for Integrative Science, W423J The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637 Tel: 773-702-4608 Fax: 773-702-6260 http://home.uchicago.edu/~emalito

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Save a transformed density map
by Keren Lasker 24 Jan '08

24 Jan '08

hello, How can I save a transformed map after using the fit map2map option? The "save map" option saves it in its original transformation. thank you, Keren.

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Chimera batch surface exporter
by Trent Grover 24 Jan '08

24 Jan '08

Hi Everyone, I'm pretty new to Chimera, but I'm working on an animation project that requires quite a few proteins and molecules. To speed up the process, I'd like to create a batch converter/exporter script to do the following: Open a PDB file Generate a multiscale model at a specified resolution Export the model out as a VRML or OBJ file I think I can do this using a Chimera command file, but I was hoping someone could point me in the right direction for some of the relevant command line syntax. Is it possible to control the multiscale model tool via command line (I know I can launch the dialog, but can I change the parameters and execute)? Is there a reference somewhere for the command line parameters for the multiscale models tool? What is the command line export command? Where can I find an OBJ exporter (there are references to it in the mailing list archive)? Any help would be greatly appreciated. Thanks, Trent BTW - I have a suggestion for improvement of Chimera. Add a command history window (or modify the existing one) that echoes out the command line text that is equivalent to any command executed via the Chimera user interface. Maya has this functionality and it is wonderful for anyone who is trying to figure out how to script a process that they know how to execute via the various menus.

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