May 2010 - Chimera-users - RBVI Mailing Lists

output data from findclash
by Kim, Sunghoon 10 May '10

10 May '10

I'm trying to see clashes of a specific sidechain with its rotating chi angles using 'findclash' command in python script. At this point, because I 'm just looking for a set of rotamers that doesn't have any contacts or clashes, I just want to see the number of contacts from a set of specific rotameric states, rather than a detailed information. But I don't know how to print 'the number of contacts' together with its corresponding chi angles. Is there any way to write a output file from findclash calculation? Or can I modify reply log as I want ? Thanks, Sunghoon

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Re: [Chimera-users] presets, python and printing
by Greg Couch 10 May '10

10 May '10

On 05/09/2010 07:51 AM, Daniel Gurnon wrote: > Hello everyone, > My colleague and I are planning to incorporate 3D physical models into > the introductory biochemistry course at our university, and I want > students to use Chimera in the design of models. I've seen the > technotes on 3D models made by the uPrint printer > (http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html). We'll > hopefully be collaborating with the folks at MSOE on this, using their > Z-corporation printer. They use RasMol to design models, but the file > read by the printer is in .stl format. > > Here are my questions: > 1) Has anyone used Chimera to create models to be printed on a Z-corp > printer? (if yes, I'll have many more questions for you...) If you are using a Z-corp printer, you should look into sending it chimera's VRML output. That is because chimera's STL output works well when you limit it to surfaces and ribbons, but the triangles generated for bonds and atoms (interpenetrating cylinders and spheres) confuse some printer's software. The Z-corp printers come with their ZPrint software that accepts VRML and should do the proper triangulation for their printers (I say "should" because we've never tested it, but from everything I've read, I expect it to work). - Greg

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Volume covered by a group of atoms
by Miguel Ortiz Lombardia 10 May '10

10 May '10

Dear all, I would like to represent as a volume the space that would be covered by a set of atoms that are bound by "torsionable" bonds when one systematically modifies those torsion angles. An example would be the side-chain of an amino acid; imagine I would like to have a glimpse of what part of the space could be occupied by that side-chain. As a first approximation I wouldn't care about clashes. I would appreciate if someone can point me to an existing way of obtaining such representation or to an algorithm that could be implemented within chimera (which I would be happy to share with other interested people; if I manage to code it, that's it!) Cheers, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

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Ensemble Cluster via command line
by Jan H. Löhr 10 May '10

10 May '10

Dear Chimera users, I have been using the Ensemble Cluster tool to cluster a set of PDB-files. Now I would like to do this via command line or python script without GUI in order to run it multiple times. However, it seems the Ensemble Cluster tool cannot be used via command line. The only thing I have been able to is to load it up with 'start Ensemble Cluster'. Is there a way to access the tool via command line? Or is there a way to record my mouse actions and translate them to commandline-style? Here are the steps I am trying to do: Load PDB-file (multiple models in it) Start Ensemble Cluster Parts to Match: :xxx-yyy (optional) OK Write List of modelnames/cluster End This can be done by mouse, but apparently not by commandline, can it? Thank You Jan Univ. Hamburg, Germany

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presets, python and printing
by Daniel Gurnon 10 May '10

10 May '10

Hello everyone, My colleague and I are planning to incorporate 3D physical models into the introductory biochemistry course at our university, and I want students to use Chimera in the design of models. I've seen the technotes on 3D models made by the uPrint printer ( http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html). We'll hopefully be collaborating with the folks at MSOE on this, using their Z-corporation printer. They use RasMol to design models, but the file read by the printer is in .stl format. Here are my questions: 1) Has anyone used Chimera to create models to be printed on a Z-corp printer? (if yes, I'll have many more questions for you...) 2) Is it possible to define a user preset in Chimera with Python? I know this isn't currently possible with chimera commands, and I am *just* getting into Python now. Because students have difficulty jumping in to a project like this if they first have to learn to enter commands at a prompt, I want to make some presets that apply settings compatible with a 3D model; bond thickness, colors, etc. 3)If one knew Python, would it be possible to design a simplified user interface for Chimera? Even as simple as a pop-up window that contained the key features I want students to have access to right away? 4) Probably the biggest drawback to using Chimera with undergrads is the lack of an "Undo" button. I'm guessing this is extremely difficult to implement because of all 3rd party extensions incorporated into Chimera? What about an option to autosave every five or ten minutes? Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Fwd: presets, python and printing
by Yang, Zheng (YZ) 10 May '10

10 May '10

Begin forwarded message: > From: "Yang, Zheng (YZ)" <yz(a)cgl.ucsf.edu> > Date: May 10, 2010 12:55:03 AM PDT > To: Daniel Gurnon <danielgurnon(a)depauw.edu> > Subject: Re: [Chimera-users] presets, python and printing > > Dear Dan, > > I am using Chimera output STL files, then print out with a uPrintPlus 3D printer. It's pretty handy using the "Export Scene" function to convert models into STL files. Although each single part cannot have mixed color, the printer is capable of printing 8 color APS by changing the cartridge. I have tried various protein representations: surface, ribbons showing the secondary structures, etc. All of them work prefect. > > By going over the Getting Started tutorial (http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html), users can easily get familiar with Chimera. Your students can use either GUI or command line mode. Alternatively, you can prepare them a Chimera commands file (plain text scripts file), containing your preset, bond thickness. (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/indexcommand.html#c…) They just need to open and load it. > > Chimera has the Undo Move function, allowing backtracking through the most recent model positions. (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/undomove/undomove.…) Section saving may solve part of the "Undo" problem. > > Looking forward to collaborating with you on the 3D model printing. > > Best, > YZ > > > > > > > > On May 9, 2010, at 7:51 AM, Daniel Gurnon wrote: > >> Hello everyone, >> My colleague and I are planning to incorporate 3D physical models into the introductory biochemistry course at our university, and I want students to use Chimera in the design of models. I've seen the technotes on 3D models made by the uPrint printer (http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html). We'll hopefully be collaborating with the folks at MSOE on this, using their Z-corporation printer. They use RasMol to design models, but the file read by the printer is in .stl format. >> >> Here are my questions: >> 1) Has anyone used Chimera to create models to be printed on a Z-corp printer? (if yes, I'll have many more questions for you...) >> >> 2) Is it possible to define a user preset in Chimera with Python? I know this isn't currently possible with chimera commands, and I am *just* getting into Python now. Because students have difficulty jumping in to a project like this if they first have to learn to enter commands at a prompt, I want to make some presets that apply settings compatible with a 3D model; bond thickness, colors, etc. >> >> 3)If one knew Python, would it be possible to design a simplified user interface for Chimera? Even as simple as a pop-up window that contained the key features I want students to have access to right away? >> >> 4) Probably the biggest drawback to using Chimera with undergrads is the lack of an "Undo" button. I'm guessing this is extremely difficult to implement because of all 3rd party extensions incorporated into Chimera? What about an option to autosave every five or ten minutes? >> >> Thanks >> Dan >> >> -- >> ____________________________ >> >> Daniel Gurnon, Ph. D. >> Assistant Professor of Chemistry >> DePauw University >> Greencastle, IN 46135 >> >> p: 765-658-6279 >> e: danielgurnon(a)depauw.edu >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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superimposed 3D structure
by deeba noreen 08 May '10

08 May '10

I am trying to make superimpose two similar proteins. To evalute its structural differences regarding functional aspects, I want to derive a superimposed model. I am using Chimera format... Can you please tell me in terms of commands so i can apply.

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ligand comformation clustering
by Maurice Ho 06 May '10

06 May '10

Hi there, How to cluster the different conformations of a ligand after a docking experiment according to their relative orientations in the binding pocket? Any software can help to do so? I've tried the Ensemble Cluster function in Chimera but it seems clustering the different conformations according to the relative positions of the atoms of the ligand itself. I know that the command rmsd #0.1:UNK #0.2:UNK (UNK is the ligand) could be a way to illustrate how distant in average between different conformations. How could I make use of this command in script so that I could have all the possible comparisons and cluster them in a sensible way? Best regards, Maurice Ho

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Re: [Chimera-users] Sequential stereo
by Greg Couch 05 May '10

05 May '10

(Forgot to cc the list.) Chimera already works with NVidia's 3D Vision, in Windows XP/Vista/7 and Linux, as long as you have a 3D Vision supported Quadro FX card, see <http://www.nvidia.com/object/quadro_pro_graphics_boards.html> for details. Since chimera does stereo within a window, the GeForce cards are not supported. FYI, the latest NVidia drivers, version 197.59, have a bug that affects chimera stereo, so you'll need to use an earlier version of the driver (or presumably a latter version which has the bug fixed). When working with chimera in stereo, you really want a display that shows full resolution left and right eye images, and that generally means that the display refreshes at 120 Hz for 60Hz per-eye (100Hz would work too). If they don't support 120Hz, then the left and right eye images are interlaced when transmitted to the display and adjacent pixels can end up being shown in opposite eyes. And that makes 2D text, like the text in labels or dialogs, very fuzzy until you take the glasses off, but that makes the 3D fuzzy. That is annoying, but if the display is cheap enough, you might be able to live with it :-). For large groups of people, the cost of the active glasses becomes significant (and maintaining the batteries is a chore). So for a large display, I'd recommend considering a technology with passive glasses, like the RealD LP, <http://www.reald.com/Content/proProducts.aspx?pageID=122>, and the DepthQ Polarization Modulator, <http://www.depthq.com/modulator.html>. They are setups for a projector that polarizes the light onto a silver screen (that reflects polarized light coherently) and you use cheap polarized glasses to view the content (same glasses as a movie theater with RealD 3D). And if you use this technology, then you have the option of using a NVidia Quadro FX graphics card or an ATI FirePro graphics card (only the V8700, V8800, and V8750 have stereo DIN connectors). Hope this helps, Greg On 05/05/2010 08:47 AM, Daniel Hitchcock wrote: > Howdy, > > My advisor was interested in setting up a large display (52" screen) > with a computer controlling it for viewing and presentation of > structures in chimera. I have been commissioned to purchase the > hardware, and naturally I want to take it a step further. > > With new "3D Ready" LG and Samsung displays (as opposed to regular > >120Hz displays) they supposedly have an extra chip to properly sync > with an incoming 3D signal from a device, be it a bluray player or > whatever. Nvidia has begun to work on their system and promises a > software update to their 3Dvision line which would allow for the > native signal to be sent to the screen as opposed to just sending a > sequential 2D signal. My questions (if that all made sense), > > 1. Is there or will there be support for nvidia's 3d Vision line? We > will be running windows 7 and the program itself will be run in > windowed mode probably, not always full screen. > > 2. If that does not work, what would be the best recommendation for > some sort of stereoview (prefereably sequential) on a large LCD or > plasma display? > > > Thanks for the help! > -Daniel Hitchcock

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Sequential stereo
by Daniel Hitchcock 05 May '10

05 May '10

Howdy, My advisor was interested in setting up a large display (52" screen) with a computer controlling it for viewing and presentation of structures in chimera. I have been commissioned to purchase the hardware, and naturally I want to take it a step further. With new "3D Ready" LG and Samsung displays (as opposed to regular >120Hz displays) they supposedly have an extra chip to properly sync with an incoming 3D signal from a device, be it a bluray player or whatever. Nvidia has begun to work on their system and promises a software update to their 3Dvision line which would allow for the native signal to be sent to the screen as opposed to just sending a sequential 2D signal. My questions (if that all made sense), 1. Is there or will there be support for nvidia's 3d Vision line? We will be running windows 7 and the program itself will be run in windowed mode probably, not always full screen. 2. If that does not work, what would be the best recommendation for some sort of stereoview (prefereably sequential) on a large LCD or plasma display? Thanks for the help! -Daniel Hitchcock

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Chimera-users May 2010