- Chimera-users - RBVI Mailing Lists

Chimera on Linux PPC
by Tom Goddard 05 Dec '08

05 Dec '08

Hi Justin, We do not currently build Chimera for Linux with PowerPC processors. Chimera includes more than 30 third-party libraries which we build automatically on each supported platform (Windows, Mac, Linux...). Compiling all those libraries is the real problem. Many of those libraries require special patches to build on all our platforms (Windows, Linux, Mac). It would likely take weeks of work for Linux PPC for someone very experienced in compiling open source packages from source code. We do not have the resources to do that for such an obscure platform. The next platform we will likely support is Mac 64-bit (Intel) sometime in the next year, after that 64-bit Windows. The latest Chimera can be compiled without the proprietary molecular surface code. We don't have that latest source code on the web site, but if you manage to build all the third-party packages (called "foreign" packages on our source code download page) I'd put the latest source code on the web and tell you how to disable the molecular surface compilation. Tom Justin A. Lemkul wrote: > > Dear Sir, > > I am installing a few machines in our lab that are running Ubuntu > Linux (8.04) on PowerPC architecture. They are iMac G5 desktop > machines, a little old, but new to us. I have thus far been unable to > install Chimera on these machines, being that it is such an odd setup, > and PPC is rapidly falling out of use. I came across a message in the > chimera-users archive that made me wonder if installing Chimera on > these systems was even possible: > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-December/000607.html > > Are you aware of anyone that has installed Chimera on such a system? > Do you think it is even possible? We would really like to be able to > use Chimera on these machines (it is installed on all our other > machines, and has become a staple in our lab). Any advice you could > give me would be greatly appreciated. > > If I can resolve all of the dependencies, would Chimera install > without MSMS? I don't believe I can install MSMS on these machines, > given the available installation packages. > > Thank you very much for your time and attention. > > -Justin >

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Vista Video Card Error
by Devon Cayer 04 Dec '08

04 Dec '08

Hello, I'm currently attempting to model some viral capsid proteins using your software. Unfortunately, when I attempt to use the "side view" option I get a video card error, and I'm told to update my video card drivers. I've contacted the manufacturer and they have told me my laptop, a Gateway MT6821, is up to date with all the latest drivers. What else could be a possible problem do you think? I look forward to any input, Sincerely, Devon C Devon M Cayer Graduate Student The Scripps Research Institute Ghadiri Lab devcayer(a)scripps.edu

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building a alpha helix
by Anindito Sen 04 Dec '08

04 Dec '08

Dear All I was wondering if there is any tool by which can generate an alpha helix, as an extension of a truncated crystal structure docked in the density map. The possibility of the truncated portion of the protein behaving as an alpha helix has been predicted by different groups. The density map shows some empty regions (after the crystal structure has been docked) just good enough for an alpha helix to fit in. Best Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Transparency of ribbons
by lvyuan zhang 04 Dec '08

04 Dec '08

Hi all, I'm a new user and my question maybe a little weird to you guys. I want to make some parts of my protein, let's say "A", partially transparent, so when compared to other parts of the protein, let's say "B", these "A" parts are hardly visible (the background is white). So I set the alpha value of "A" to less than 1, such as 0.1. then I save the image with POV-ray. The resulted "A" is too dark, and it is still quite "visible". Is there any way to make partially transparent ribbons lighter, instead of darker than non-transparent ones? I would really appreciate it if any one can help resolve this problem. Thans! Cheers! Luyuan Zhang

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Software(Drug Design)
by Tarit Mitra 04 Dec '08

04 Dec '08

28, Ashfield Green Yateley Hants GU46 6AL UK Dear Sir, I am a retired scientist, and working on an honorary basis for the University of London. I work from home and go to the University in regular interval. I would very much like to use your software for drug design. I was wondering whether you would grant me a free academic licence to the software. I shall only use the software for academic purpose and not for any financial reason whatsoever. I have both Linux(Ubantu) and Windows XP. My computer has 40GB hard disk with 756MB RAM I shall be grateful if you will kindly consider my case favourably. Yours faithfully T. K. Mitra, B.Sc(London), Ph.D(London)

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opaque background
by Mueller, Juergen-Joachim 01 Dec '08

01 Dec '08

Dear all, is there a possibility to make the background invisible to be able to overlay a structure over anything? Thanks, Juergen

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Chimera rotational matrix
by Bui Khanh Huy 01 Dec '08

01 Dec '08

Hi, I notice that Chimera has slightly different in calculation of transform when I tried to rotate my EM density (200x200x200 mrc file) using Chimera. The origin of the density reported by Volume Viewer is 0,0,0 First, I print out the homologous transform matrix using: >>> om = chimera.openModels >>> mlist = om.list() >>> m = mlist[0] >>> print m.openState.xform The transformation is: 1 0 0 0 0 1 0 0 0 0 1 0 If I rotate the model using command: roll z -30 1 Then print out the transform matrix again: 0.866025 0.5 0 -36.8852 -0.5 0.866025 0 61.2937 0 0 0 1 That would be weird because I didn't do any translation. So what is really happening in Chimera when I rotate the model? Best, Huy

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How to generate submodels in a mol2 file in Chimera?
by CHIU,YEUNG 01 Dec '08

01 Dec '08

Dear friends, Hello! I'm wondering how many models and submodels in all can Chimera save into one single mol2 file? Right now I can have models only 0-9 into one single mol2 file. I think I'm going to use submodels, but how can I generate them? For instance, if I have a brunch of pdb files which contain one molecule each, I'd like to combine them into one mol2 file, which has a submodel corresponding to each molecule. (If this statement of the problem is not clear enough, please let me know). Thank you for your help and sorry to bother the others. Best wishes. Sincerely yours CHIU,YEUNG

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Increases size of labels
by Todd Weaver 25 Nov '08

25 Nov '08

Under the Actions pulldown for Label --> Other is there a way to increase the size of the lettering/numbering. When I make side by side stereo the labels are too small for publication. Thanks so much! -- Todd M. Weaver, Ph.D. UW-La Crosse 1725 State Street Chemistry Department 4020 Cowley Hall La Crosse, WI 54601 Ph. (608)785-8269 Fax (608)785-8281

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Laplacian filter on density maps
by Grigore Pintilie 24 Nov '08

24 Nov '08

Hi, Just wondering if it might be possible to apply a Laplacian filter on a density map in chimera. The reason I'm asking is that if the cross-correlation is computed with laplacian-filtered maps it gives more robust results for the correct alignments vs. non-correct alignments. Thanks, Greg

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