January 2005 - Chimera-users - RBVI Mailing Lists

re H-Bonds in ViewDock
by Vidana.Epa＠csiro.au 02 Feb '05

02 Feb '05

Hi Chimera users, I've started to use Chimera recently. When using ViewDock it struck me that it would be very useful, after loading a .mol2 file of ligands and computing H-bonds between them and the receptor, to be able to list the number of H-bonds as a column in the ViewDock ListBox. Or, is it somehow possible to do this already? (One way to fix this might be to have a script that will write the number of H-bonds computed for each molecule in a new .mol2 file, and then read in this modified .mol2 file .... Has anybody done something in this fashion?) Thanks very much. Cheers, Vidana. Vidana C. Epa CSIRO, Division of Health Sciences & Nutrition, 343 Royal Parade, Parkville, Victoria 3052, AUSTRALIA. tel.: (61) - 3 - 9662 - 7345 fax.: (61) - 3 - 9662 - 7347 email: Vidana.Epa(a)csiro.au

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[Chimera-users] Defining Attribute Color for Surface Independent of Atoms
by David Piper 25 Jan '05

25 Jan '05

Chimera Folks, I have set up a file to define a series of colors based on functional measurements for some residues in a PDB file. I would like to color the ball and stick atoms according to element type and a semi-transparent surface according to the colors defined by my text file. It seems like these two things are tied together; that the surface can either be colored by the model, the atoms, or a specific color. Can I color it according to a Defined Attribute but leave the atoms as CPK coloring? Thanks, David

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chimera --stereo crash
by Liu, Hao-Yang 24 Jan '05

24 Jan '05

Dear Sir/Madam, I am running chimera in IRIX, and when I am trying to run "chimera --stereo", I got this message: Unable to find hardware stereo support (Togl: couldn't get visual) and when I click ok, the program just quit. I can use the normal (mono) mode in chimera. and I think I had the hardware, because I use midas a lot, and never had problem in midas. Could you tell me how can I use the stereo mode in chimera? What am I missing? Thanks Hao-Yang Liu

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selecting
by John Nixon 18 Jan '05

18 Jan '05

Hi folks, I'm a newbie and am having trouble getting started. Sorry to be dense. Using the command line on a single protein chain O select :32-42,44-49.O or rep sphere :43:56:59:60:61:63:65:67:68:70:71:72:73:74:75:78:110:113.0 only seems to work on the last residue. Thus I'd have to write a separate command for each residue. Could you tell me what I've missed please! John

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[Chimera-users] FW: [PyMOL] Stereo-3D in a Window: Not in MacOS X Tiger?!!
by Warren DeLano 14 Jan '05

14 Jan '05

Greetings Fellow Vendors and Software Developers! Is stereo 3D graphics support on MacOS X something you would like to see soon? If so, then please take just 30 seconds to respond to the following petition. We've received more than 300 compelling responses over the past 18 hours about the importance of supporting stereo 3D graphics today -- but we will need more to convince Apple, so please consider participating. It is as easy as clicking this following link, adding a few words with your personal perspective on the issue, and then hitting send! mailto:warren@delsci.com&subject=Stereo%203D%20Matters%20to%20Me%21 Cheers, Warren -----Original Message----- From: pymol-users-admin(a)lists.sourceforge.net [mailto:pymol-users-admin@lists.sourceforge.net] On Behalf Of Warren DeLano Sent: Thursday, January 13, 2005 5:59 PM To: pymol-users(a)lists.sourceforge.net Subject: [PyMOL] Stereo-3D in a Window: Not in MacOS X Tiger?!! Fellow Visualization Software Users: My #1 gripe with MacOS X Panther has been the lack of support for industry-standard stereo-3D graphics (in a window). So far, I and others have been unable to convince Apple that this feature matters enough to their bottom line to merit implementation. Candid discussions this week at MacWorld confirmed that Tiger (OS X 10.4) will likewise ship without this essential capability at a time when the opportunity for Apple is at its peak in this market. I believe this would be a serious error, and that Apple must now hear from us on this issue. If you agree, then please reply directly to me, RIGHT NOW (mailto:warren@delsci.com) with the words: "Stereo 3D matters to me." Your response will be printed, and I will hand-deliver them to Apple management in nearby Cupertino at the end of the month. We need AS MANY responses as we can get (ideally 1,000+), so please forward this email to all of your visualization-oriented colleagues (in any sector), and ask them to submit individual emails to me as well. Here's why: Stereoscopic 3D visualization increasingly matters in science, medicine, and engineering. Though arguably the ultimate technical computing platform, the Mac remains hopelessly crippled in this key respect when compared to Sun, HP, Dell, or IBM workstations running Linux, Solaris, or even Windows. Dual-Xeon and dual-Opteron systems now ship stereo-3D-ready thanks to powerful nVidia/Quadro and ATI/FireGL graphics cards. Thus, the competition WILL OWN THIS MARKET if Apple doesn't support stereo-3D in a window on MacOS X, ASAP. The disruptive market opportunity created by the implosion of SGI and the stopgap adoption of "home brew" Linux systems is about to end. Professional-grade stereoscopic visualization is now a standard OpenGL capability, it is vendor-supported on a variety of hardware, and it is present on every platform EXCEPT THE MAC. None of those "amazing features" in Tiger matter one bit to technical users whose basic needs remain unmet. Stereo-3D inadequacy is a show-stopper for many scientists and engineers. The Mac will not have a fair shot at this market unless Apple quickly follows though on it's assumed responsibility to support all OpenGL features, including quad-buffered stereo-3D graphics in a window. Case in point: my company just spent $5k on a dual-Opteron Sun workstation instead of a dual-G5 Mac solely because stereo-3D in a window is absent from MacOS X. This pattern will surely be amplified many thousand-fold if Apple does not take immediate corrective action. Responding together, we can insure that Apple understands what this deficiency means for the future of MacOS X in scientific, medical, and technical visualization. I do not believe that Apple management has made an informed decision regarding stereo-3D, and I think this is our last best chance to change things before the issue becomes moot. Please share your concerns by responding to this email (mailto:warren@delsci.com). It will only take a second, but the benefits could last for years to come if Apple listens well and then acts decisively. Input from current Linux and Windows users is especially welcome, since Apple would love to sell you the visualization platform of your dreams if you're willing to help define it. Thank you for your time. Cheers, Warren Author of PyMOL: http://pymol.sf.net (Note that MacPyMOL is currently shown on http://apple.com/science under "The Tools" -- cool!) DeLano Scientific LLC company profile: http://delanoscientific.com/about.html PS. An alternate way to be heard is to post on the Apple SciTech or Sci-Vis mailing lists, but please CC me too to be sure that you're counted. http://lists.apple.com/mailman/listinfo/scitech http://lists.apple.com/mailman/listinfo/sci-vis -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren@delsci.com ------------------------------------------------------- The SF.Net email is sponsored by: Beat the post-holiday blues Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek. It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt _______________________________________________ PyMOL-users mailing list PyMOL-users(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users

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Re: [Chimera-users] Mol2 Trajectory Reader?
by Eric Pettersen 06 Jan '05

06 Jan '05

Hi Joshua, Given that what you really want to do is assemble a movie of your conformations rather than actually analyze them as a trajectory, what we've decided to do is write an extension that will allow you to record whatever is going on in Chimera as a series of frames (it will have a "Start" and a "Stop" button) and will assemble those frames into an mpeg. It will optionally allow you to keep the frames in case you want to assemble them into a format that is harder for us to support across all platforms (e.g. Quicktime), and may also support generating an animated GIF. A preliminary version will probably be done in a couple of weeks and we could send that to you if you want to be a guinea pig. Otherwise, it will be in the next release, which will probably be April or so. --Eric On Dec 25, 2004, at 8:15 PM, S Joshua Swamidass wrote: > Good point. > > I didn't notice the move menu. The ultimate goal of all this for me is > to literally make some movies, either with screen shots in sequence or > ideally if chimera can output an avi automatically. So i guess, > viewdock should work IF there is a way to capture all the images to > disk rather than just play them to the screen. > > S Joshua Swamidass > > > On Sat, 25 Dec 2004 09:29:55 -0800, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: >> Hi Joshua, >> Implementing the Mol2 trajectory format looks perfectly doable >> with >> the data file you provided. Before proceeding with the work, I guess >> I >> have a question as to why you want to use the molecular-dynamics Movie >> tool on the file rather than ViewDock tool. You do know that the >> ViewDock tool has a "Movie" menu >> (http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ >> viewdock/viewdock.html#movmenu) that allows you to step through docked >> conformers one by one? I guess I'm trying to determine if I should >> really be adding this fomat to the Movie tool or if we should somehow >> be improving the capabilities of ViewDock instead. >> >> --Eric

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Just fixed Re: [Chimera-users] WinXP SP1 python error on File -> Open
by Li Wang 04 Jan '05

04 Jan '05

Dear all, I forgot to attach the python code in my previous email. Please let me know if there is anything wrong with the code. By the way, I am using the Chimera beta version 1, build 1917, 2004/03/08. Should I download the newer version, version 1 build 2065? Thank you so much for your help in advance. Li

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Just fixed Re: [Chimera-users] WinXP SP1 python error on File -> Open
by Li Wang 04 Jan '05

04 Jan '05

Dear Eric, I just join the Chimera-users discussion group and haven't got reply email. However I checked the archive and found your reply email related to the WinXP SP1 python error on File -> Open. I have been using Chimera to generate the colorful ribbon picture for the pdb file using command line. Now I am tring to figure out the general way of defining the bfactor range corresponding to the different colors. I found the flexible python code for making the rainbow color by bfactor and tried it out. But it ended up with the file/open error message as I didn't see any problem in the code. Attached please find the copy of the python code. I did replace bo and b1 by min and max of bfactors in the pdb file. Your help and suggestion are greatly appreciated. Li Wang Biomedical Informatics of OSU Columbus, OH (w) (614)688-3236

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Chimera-users January 2005