July 2010 - Chimera-users - RBVI Mailing Lists

Fwd: Visualizing inertia axes as arrows
by Eric Pettersen 31 Jul '10

31 Jul '10

Hi Miguel, Thanks for the corrections! I just fired that one off without testing it. I thought there might be an error or two. I'm glad you find it useful after fixing it. --Eric Begin forwarded message: > From: Miguel Ortiz Lombardía <miguel.ortiz-lombardia(a)afmb.univ-mrs.fr> > Date: July 31, 2010 1:39:33 AM PDT > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Visualizing inertia axes as arrows > > Hi Eric, > > Thanks for this useful script! > > I think I found two errors though: >> >> from chimera.selection import currentAtoms, numpyArrayFromAtoms > > should be: > > from chimera.selection import currentAtoms > from chimera import numpyArrayFromAtoms > > and: > >> for val, vec in zip(vals, vecs): >> bildString += ".arrow %g %g %g %g %g %g .1 .2 .9\n" % ( >> centroid[0], centroid[1], centroid[2], >> centroid[0] + val[0] * vec[0], >> centroid[1] + val[1] * vec[1], >> centroid[2] + val[2] * vec[2]) > > has to be: > > for val, vec in zip(vals, vecs): > bildString += ".arrow %g %g %g %g %g %g .5 1. .9\n" % (centroid[0], > centroid[1], centroid[2], centroid[0] + val * scale * vec[0], > centroid[1] + val * scale * vec[1], centroid[2] + val * scale * > vec[2]) > > (you can ignore the scale thing, that's simply a 50/max(vals) > correction > so the longest axis is 50 A) > > Best, > > > -- > 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 > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. >

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Visualizing inertia axes as arrows
by Jozef Lewandowski 30 Jul '10

30 Jul '10

Hi everybody, Lately, I have been using "measure inertia" command a lot. For my purposes I needed to visualize the inertia axes as arrows instead of the default ellipsoid. I used the vectors from the reply log to write BILD files defining the arrows for the inertia axes. Is there an easy way to script just that? Or differently, is there an easy way to visualize as arrows inertia axes for peptide planes in a protein? Any tips would be appreciated. Thanks, Józef

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Re: [Chimera-users] about transformation matrix
by Tom Goddard 28 Jul '10

28 Jul '10

Hi Julio, I guess you are using the fitnogui.py script. http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/fitnogui.py The parameters are right near the top -- ijk_step_size_min is the one you're interested in. The initial contour level is set as described in the documentation: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… The "volume" command can set the contour level: volume #0 level 27.6 Tom > Hi Tom, > > Thanks again. Editing the line of code would be perfect for us, since we are calling Chimera from our program with the "nogui" option. Could you point me the place where I need to change that 0.01? > > What happens with the contour level when I'm calling Chimera in that way (nogui)? Can I similarly set it somewhere in the code? Or with an option in the command line? > > Best, > Julio > > > > Hi Julio, > > The details of the fitting algorithm are given in the User's Guide. > > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht… > > You should definitely read that if you want the best understanding. But > the brief answers to your questions are that the convergence criteria > looks for optimization steps of less than 0.01 grid index to decide > convergence. The user interface does not allow you to change the 0.01 > grid index criteria -- it could be done by editing a line of Python. > The default settings do mask using the contour level of the fit map as > an outer boundary. So that level is important. > > Tom > > >

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Camera parameters
by Tom Goddard 27 Jul '10

27 Jul '10

Hi Matt, The Chimera camera always points along the negative z-axis. The positions of the models are moved/rotated to get different view-points. Do you mean you want camera location (x,y,z) and horizontal angular field of view to the edges of the window (for perspective projection)? I know how to get at these using Python code, but I'm not sure if any Chimera commands report those values. Also I don't know if that info makes its way into X3D or VRML exported from Chimera. Greg Couch would know these answers. He is at SIGGRAPH this week. A quite gruesome way to get the parameters is to find them in the Chimera session file. grep formattedPositions mysession.py formattedPositions = {'p2': (0.3954088241213373, 18.749999499320985, (14.059999585151672, 7.399999618530273, 8.628906249999993), (36.02048479676247, -18.762672296762467), 8.62890625, {(0, 0): ((13.338430482851305, 2.7738552720503122, 6.309792459458727), (0.3889244976446376, 0.8937166155966246, 0.22362545950400858, 33.757570197325826))}, {(0, 0, 'Volume'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (29.312384727061698, 10.919780805124898, 8.628906249999993), False), 'p1': (1.0, 18.749999499320985, (14.059999585151672, 7.399999618530273, 8.62890625), (36.02048479676247, -18.762672296762467), 8.62890625, {(0, 0): ((-1.913954659058722, -0.7459259145443079, 6.309792459458727), (0.3889244976446376, 0.8937166155966246, 0.22362545950400858, 33.757570197325826))}, {(0, 0, 'Volume'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (14.059999585151669, 7.399999618530277, 8.628906249999993), False)} This is pretty messy and the values depend on which Chimera version saved the file. The values are defined by Python code chimera/share/Midas/__init__.py in the _savePosition() routine: return ( viewer.scaleFactor, viewer.viewSize, cam.center, cam.nearFar, cam.focal, xforms, clips, om.cofrMethod, cofr, viewer.clipping ) If you want a Python script to simply dump the camera positions for all savepos positions I can provide that. Tom > Hi Tom, > > I am creating a workaround for my graphics problem. What I have done in the past is to create a VRML file from Chimera export, extract the openGL camera parameters using a text editor, start up Amira, using TCL I would recreate the same camera view within Amira. At this point I could splice animation clips made by Chimera& Amira using Final Cut Pro. > > It has been a while since I have done this. I am now looking at the exported VRML files and they are lacking the camera info. > > Is there a command I can use to get the camera parameters for the savepos keyframes? > > thanks, Matt > >

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coordinate transformation
by Dougherty, Matthew T 27 Jul '10

27 Jul '10

I was trying to locate details on maxtrix, coordinate transformations & scenegraph, relative to camera transformations.

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about transformation matrix
by Kovacs, Julio A 27 Jul '10

27 Jul '10

Hi, I am doing fitting of two maps and am getting different values of the transformation parameters: the ones given in the window where I specify the options (these seem to be correct), and those given by using the command "matrixget" --- these give a very large translation vector, and moreover, I don't see any relation between that vector and the correct translation. Also, could you tell me what is the order used in Chimera: rotation, then translation? or translation, then rotation? Thank you very much. Julio Kovacs

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Problem
by Reza Heidari 27 Jul '10

27 Jul '10

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Nvidia 3D Vision
by "Christoph Höglinger" 27 Jul '10

27 Jul '10

Dear Chimera developers, I just bought the Nvidia 3D Vision Kit, because i was interested in the 3D Visualisation of it. First I tried it with the latest drivers from Nvidia's Homepage. (Quadro Driver Version: 258.49 & 3Dvision 258.49 ). I changed the Settings in the NV Control Panel (for Stereo output). Sequential Stereo worked fine in an other 3D Application. But when i change the view settings in chimera (sequential Stereo) i get that error: (After The Error MSG ist Quits and displays the Exit Code 3) Runtime Error! Program: C:\Program Files\Chimera\bin\pythonw.exe This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. Then i was looking for hints to solve that problem i found following article. http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005173.html There you mentioned that its probably a problem with the "new" drivers (197.XX). So I installed the driver that had been recommended by you. (Quadro Drv. 191.87 + 3D Vision 191.00). The Problem was that this 3D Vision driver won't support my LCD, its an Acer GD245HQ). I have installing it "manually" it won't activate the shutter glasses when Sequential Stereo is switched "on" in chimera (Shutter doesnt even work in games or any other Application) That means that the 3D-Vision driver is to blame. 197.03 Will recognize my LCD, but that won't work with chimera. Tried also QDRO 191.87 & 3DVision 258.49 (but theres no way to run the 3DVision Setup) Have you got an idea on how to fix that Problem? That would be really great! This is my System Configuration: Intel Pentium E5200 @ 3.5GHz PNY Quadro FX 570 4GB Ram Windows 7 64 Bit Acer GD245HQ Thank you so much for your help! Best regards, Christoph -- GMX.at - Österreichs FreeMail-Dienst mit über 2 Mio Mitgliedern E-Mail, SMS & mehr! Kostenlos: http://portal.gmx.net/de/go/atfreemail

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Directly representing ellipsoids
by Thomas Ouldridge 26 Jul '10

26 Jul '10

Hi, I'm afraid I'm not a crystallographer/protein simulator, and so this question might seem quite naive. I run coarse-grained simulations, and I would like to represent the objects as ellipses in chimera. I have the position (which I am able to use) and the orientation that I would like my ellipses to take, encoded as a matrix relative to (x,y,z) cartesian coordinates. This matrix gives me the principal axes and radii of the ellipse. As I understand, Chimera is designed to display a "Thermal ellipsoid" - I would like this ellipsoid to have the axes and radii given by my matrix. However, it seems that the input (via pdb format files) is interpreted as an "anisotropic temperature factor", and I can't find a way to convert my matrix into the anisotropic temperature factor (I tried some papers online but they seemed to be talking in terms of transformations between lab frame and crystallographic frames, but I cannot see how that applies - what is my crystallographic frame?). In short, is there a way to convert my matrix into the "anisotropic temperature factor" representation so that Chimera can read it and convert it back? I did try just plugging in the matrix elements to the PDB file but got some weird ellipsoids out. Any help would be gratefully appreciated, Tom

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Transparency doesn't look right
by Tom Goddard 26 Jul '10

26 Jul '10

Hi Mitalee This is a Chimera limitation. Two or transparent models will not be shown correctly. Transparency works correctly only when at most one model is transparent. You have the volume data displayed in "solid" style which is a kind of transparent rendering, and you have a surface model which is transparent. How defective the transparency looks depends on the order the models were opened in Chimera (or maybe it depends on which has higher model id number, don't recall). In any case, both orders look seriously wrong. If you reverse the order of opening your two models I think your surface will remain totally invisible until it becomes 0% transparent when it will suddenly appear. This limitation is a rather fundamental design problem in Chimera. Chimera draws the models one at a time. A model that is drawn after another model can only appear in front of the first model. Chimera first draws all opaque models, then draws all transparent models. If you look at the termite gut video I made http://www.cgl.ucsf.edu/chimera/animations/movies/termitegut.mov where surfaces fade in you'll see at the start of the fade in, a black blob suddenly appears representing the object. This is the same bad behavior you see in your case, but your surface is white (the background color) and is in front of the volume data making it look especially bad. This problem has arisen many times in, especially in movie making where transparency is used to fade objects in and out. I have an idea for a solution although it is not yet implemented. But we just hired Daren Weber to work on animation improvements in Chimera and perhaps he can try this. The idea is to enhance the movie command to add a "crossfade" option. You would display the volume, then use a command like "movie crossfade 25" then show the opaque surface. The command would take the image right before the command was issued and the next image and linearly blend them over 25 frames. This would be useful for many fade scenarios. It is limited in that it won't be able to have models moving and a fade occurring at the same time since that is not simply a linearly blending of two images. I'll see if Darren is interested in trying to add this if you are interested. If you do not want to wait for this, another option is to record your movie without the fade -- just have the surface suddenly appear. Then drop the movie into an video editing program like Final Cut and add the crossfade with that software. Tom > Hi Tom, > > I was using the surft command, trying to make a segment appear inside of a > cmap file. Basically, I have a cmap file open and visible, and I want to > show the segmented cell appear slowly. My problem is that when I set the > transparency of the segmented cell to 100 (i.e. surft 100 #0), it doesn't > exactly become transparent, or what I thought would be transparent. When I > enter this command, it makes the entire image transparent at that point > (so the shape of the segmented cell is preserved and matches the > background. I've attached an image of what I got as a result. Is there a > way to make preserve the cmap image and just make the segmented cell > overlay onto it without completely "removing" the section where the > segmented cell will appear? > > Thanks, > Mitalee

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Chimera-users July 2010