- Chimera-users - RBVI Mailing Lists

Chimera under KDE (update)
by Mingfeng Yang 05 May '06

05 May '06

Please disregard my previous message. I just tried to kill the KDE system process one by one and found out that skim (an input program) is the one should be blamed. Mingfeng

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Can't input anything under KDE
by Mingfeng Yang 05 May '06

05 May '06

I am using Chimera build 2199 under KDE 3.5.2, and I can't input anything into the command line (and other input dialogs) of chimera. The linux distribution is Kubuntu Dapper Drake. If I get into the KDE environment with failsafe mode, everything is fine. And I remember chimera works fine under KDE 3.5.2 under gentoo. I guess some service(s) of KDE must have confliction with chimera, but I couldn't figure out which one. :( Best, Mingfeng

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absolute scale?
by Cathy Lawson 02 May '06

02 May '06

Hi, Is there a way to set an "absolute scale" for viewing in chimera? I'm trying to make pictures in multiple Chimera sessions with different molecules and would like for the results to be all on the same scale. I naively thought I could do this with the "camera" scale but then I noticed that for two different sessions where this value was set to 1.0, the actual scales are quite different. Chimera help revealed that the camera scale is relative to the original size when the model was first opened. Any suggestions would be appreciated! thanks, Cathy Lawson *********************************************************************** Catherine L. Lawson Laboratory for Structural Biology and Bioinformatics Department of Chemistry and Chemical Biology Rutgers University 610 Taylor Road, Piscataway, NJ 08854 cathy.lawson(a)rutgers.edu tel 732 445 8074 fax 732 445 5312 http://rutchem.rutgers.edu/~lawson http://roma.rutgers.edu/~lsbb *********************************************************************

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Broken labels!
by Changhoon Kim 02 May '06

02 May '06

Hello? I am using Chimera on Windows XP. It's "beta version 1 build 2199 2006/01/24". When I tried to display residue labels, many of the labels were unrecognizable. I've attached the picture showing the broken labels. Sometimes the distance labels are also unrecognizable. I hope it would be fixed soon. Regards Changhoon Kim

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libGL.so
by Isaac Amela Abellan 02 May '06

02 May '06

Hello, I'm using Linux and when I had tried to execute chimera this message appeared: "OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1. Please read installation instructions." I said it several times to my system administrator and he solved it using your instructions (see below): "If Chimera terminates with the error OpenGL misconfiguration detected, that means that you have two different versions of libGL.so installed -- one in /usr/lib (installed by your graphics card drivers) and one in /usr/X11R6/lib (possibly installed by Mesa, which if so would mean no hardware graphics acceleration if this version were used). Reinstalling your graphics card drivers should remove the /usr/X11R6/lib version. Alternatively, you could rename or remove the /usr/X11R6/lib version yourself. With the latter approach you might want to verify that all OpenGL applications that you use continue to work before permanently removing the library. On startup, you may see the warning Xlib: extension "Xfre86-DRI" missing on display "0.0". That means that there was no graphics driver found for your card that uses the DRI, direct rendering interface, technology for fast 3D graphics. The solution is to either ignore the warning or to upgrade your hardware and software (see Mesa/OpenGL issues below)." The problem is that when I reboot my computer the problem still appears and we should do the same procedure explained above. We can't configure the system conservating the libraries of my card drivers (/usr/lib) without removing the Mesa ones (/usr/X11R6/lib). How can we solve the problem? We will be waiting for your response. -- ------------------------------------------------ Isaac Amela Abellan PhD Student Laboratory of Bioinformatics Institute of Biotechnology and Biomedicine (IBB) Autonomous University of Barcelona (UAB) 08193 Bellaterra, Barcelona. Spain. Phone: 34-93-5812807 e-mail: iamela(a)bioinf.uab.es ------------------------------------------------

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Stereo angle value
by Prof. Fabrizio Briganti 02 May '06

02 May '06

Hi, I have not been able to find any reference to the value for the angle difference between Right and Left views in Stereo Images made with Chimera. Can you help me find it? Is there any way to change such angle value? Thanks Fabrizio

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Paper virus models
by Thomas Goddard 02 May '06

02 May '06

I made a Chimera tool that flattens icosahedral virus models. Printing, cutting, folding, and taping produces a paper model. http://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.h… The flatten icosahedron tool can be downloaded from the Chimera experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Tom

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writing mrc files
by Eran Shacham 21 Apr '06

21 Apr '06

Hey there, I am trying to write an mrc file using the write_mrc2000_grid_data module. My function is below. My array of data is a <scitbx_array_family_flex_ext.double object at 0x58b9502c>. Which is a basically a matrix with dimensions: (243, 243, 243). When trying to write an mrc file using this array I get the following error: ************************* File "/home/eshacham/cctbx/mrc_functions.py", line 20, in write_mrc write_mrc2000_grid_data(g, path) File "CHIMERA/share/VolumeData/mrc/writemrc.py", line 44, in write_mrc2000_grid_data File "CHIMERA/share/VolumeData/arraygrid.py", line 48, in submatrix ValueError: need more than 1 value to unpack Code used *********************** def write_mrc(data): print data origin = (1.54, 2.45, 3.45) # XYZ coordinates of array index (0,0,0) step = (.25, .25, .25) # Spacing between grid points import Numeric a = Numeric.array(data, Numeric.Float32) arrays = [a] import VolumeData g = VolumeData.Array_Grid_Data(arrays, origin, step) path = '/home/eshacham/structures/result.mrc' from VolumeData.mrc import write_mrc2000_grid_data write_mrc2000_grid_data(g, path) I am assuming that it has to do with my array dimensions. Any help would be greatly appreciated. Cheers, Eran.

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Re: [Chimera-users] Rotation about an axis
by Thomas Goddard 21 Apr '06

21 Apr '06

Hi Jordan, Aha! It turns out I wrote code that does exactly what you want last year. It is called the symmetric molecule copies command at the bottom of the Chimera experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html It is not distributed with Chimera yet but you can download it on that page and install it with your existing Chimera. I hate to discourage you from Python programming in Chimera but I think this is just what you need. You open one copy of your molecule and then use this "sym" command to make the hexamer. Then when you move the original copy of the molecule relative to your map, the other 5 copies automatically reposition to maintain the 6-fold symmetry. To get a more detailed description look at the "details" link on the experimental features page. The hexamer symmetry comes from the BIOMT matrices in the PDB file. This sym command treats those matrices in the coordinate system of the density map (yes, a bit weird). The key here is to make sure the symmetry axis of the density map matches the symmetry axis of the BIOMT matrices. The easiest approach is probably to make the BIOMT matrices produce a hexamer about the z-axis through (0,0,0). When you open your density map in Chimera it may not have the hexamer density centered at (0,0,0). You will need to adjust its origin so the density hexamer is centered at (0,0,0). Use the volume dialog menu entry Features / Origin and Scale to adjust the position of the lower left front corner of the map. Assuming the hexamer is centered in a 128 x 128 x 100 grid with voxel size 0.8 angstroms you would set the origin to (-50.8, -50.8, -39.6) = (-63.5 * 0.8, -63.5 * 0.8, -49.5 * 0.8). The weird 63.5 = 128/2 - .5 instead of 64 = 128/2 is easiest to understand if you think of a map that is only 2 by 2 by 2 in size. Remember to press the Enter key in one of the origin fields in the volume dialog to have the new position take effect. In any case that may still be a half voxel off depending on your map, or it may be way off. Of course you have to know the position of the center of the hexamer in your density to make this work. A way to verify that you have set the correct origin is to open 2 copies of the map -- set the map origins, then use constrained move to rotate just one copy keeping the other one fixed. It is easy then to visually see if the two copies are concentric. For convenience you can save your map as an MRC file with the new origin with the volume dialog File / Save As... menu entry. Saving a Chimera session also saves the origin in the Chimera session file (the map is not modified). I can see various troubles with using the Multiscale tool. First Multiscale low resolution surfaces are not reliably synchronized to the individual PDB models. If you change a PDB model position Multiscale won't realize it and the low resolution surface will not move to the new location. If you are using the latest Chimera snapshot (1.2224, April 10, 2006) then the problems will be even more severe because I changed the way Multiscale positions PDB models. Instead of setting the pdb_model.openState.xform it changes the atom coordinates of the model (setting atom.coord = x,y,z). All the xforms of the 6 models in a hexamer would be the same in Chimera 1.2224. This change was made to allow correctly moving individual chains of multiscale models, possible with the "movement mouse mode" feature on the experimental features web page. Lastly some clarification about Chimera's coordinate systems. First there is a global Chimera coordinates system with the x axis always horizontal relative to your graphics window, the y axis always vertical, and the z axis always pointing out of the screen at you. When you rotate models with the mouse, this coordinate system does not change -- the individual matrices positioning the models are changed. The origin of this global coordinate system is not necessarily in the center of the screen. It can be anywhere including off-screen. The global coordinates for the center of the screen are set to match the center of the bounding box of the first model you open in Chimera. Besides the global coordinate system each model has a local coordinate system. With a PDB file, the atom coordinate positions are in the local coordinate system. If you open a PDB model in Chimera and rotate it, the atom.coord x,y,z values do not change -- they are expressed in the local coordinate system which is fixed to the atoms and rotates with the model. (You can however change the atom.coord positions using Python code.) The pdb_model.openState.xform 3 row by 4 column matrix gives the rotation and translation that maps the local coordinates (e.g. a PDB atom position) into Chimera global coordinates. Other types of Chimera models like density maps are just like PDB models having a local coordinate system -- the density map grid points have unchanging coordinates in the local coordinate system. More than you wanted to know. Tom > Date: Thu, 20 Apr 2006 19:51:40 -0700 > From: "Jordan Benjamin" <jordan.benjamin(a)gmail.com> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Rotation about an axis > > Ah, it looks like it still works for normal models. The weird behavior > was with a model that had been generated with the Multiscale Models > tool from crystal contacts. I still wish I understood the > global-vs-local issue better though. > > > On 4/20/06, Jordan Benjamin <jordan.benjamin(a)gmail.com> wrote: > > Thank you for your help on this. I have a further question. Basically, > I'm trying to dock into electron density the crystal structure of a > protein that forms a hexamer. I would like to be able to have six > copies of the monomer structure loaded at once, and when I move or > rotate one copy, I'd like to be able to transform the other five to > match. So, I thought the ConstrainedMove code would be a good starting > point, since what I'm trying to do is the same thing it does, just > with the rotation specified by degrees instead of by dragging the > mouse. > > After you sent the email below, I modifed the function I was writing > accordingly, and it worked. However, I'm trying to use it now, and > it's not working. I'm a little lost on debugging it, because I don't > even know what Chimera's concept of a global coordinate system is, nor > do I have any way to visually display the local origin and axis for > each object. Is there a way to do these things that you know of? Do > you know of a simple way to rotate an object X degrees around a > specified axis (relative to another object if needed)? > > If these are really hard questions and the answer is just that I > should read the source code until I figure it out, that's totally > fine. I just thought I'd ask. > > At least with Chimera the code IS available, unlike the situation with > Amira where things would be undocumented and broken, and there'd be no > way to fix them... > > Thanks so much, > Jordan > > The function I was using is as follows (yes, it's brittle and ugly, > but it's all I had time for): > def update_hexamer(ref_model,model,*rest): > origin = (0,0,0) > axis = (0,0,1) > angle_deg = 60 > > mvo = chimera.Point(*origin) > vo = ref_model.openState.xform.apply(mvo) > mva = apply(chimera.Vector, axis) > va = ref_model.openState.xform.apply(mva) > > xf_original = model.openState.xform > > for i in range(5): > xf = chimera.Xform() > xf.translate(*vo) > xf.rotate(va, angle_deg+60*i) > xf.translate(-vo.x, -vo.y, -vo.z) > model.openState.globalXform(xf) > rest[i].openState.xform = model.openState.xform > model.openState.xform = xf_original >

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Re: [Chimera-users] Sum of volume data values
by Thomas Goddard 13 Apr '06

13 Apr '06

Hi Eran, Ok, here is code to read an MRC file and print the sum of map values without using Chimera. You need Python, the Numeric Python module which handles multidimensional arrays and the VolumeData module from Chimera. Numeric is obtained from sourceforge: http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=1351 The VolumeData module is in your Chimera distribution. chimera/share/VolumeData Here's an example running the script where I've set PYTHONPATH to have access to the VolumeData module: % env PYTHONPATH=/usr/local/chimera/share python2.4 volumesum2.py Sum of values of groel.mrc = 21720.8984375 Send future questions to chimera-users(a)cgl.ucsf.edu so others who have similar problems can benefit. I get that email just as fast. Tom ------- file volumesum2.py follows: # Script to print the sum of volume data values. # Does not need Chimera, just the VolumeData module and Numeric and Python. path = 'groel.mrc' # Read the MRC volume data and get the 3-D Numeric array. from VolumeData.mrc.mrc_format import MRC_Data data = MRC_Data(path) m = data.matrix() # Compute the sum of the elements of the volume matrix. import Numeric sum = Numeric.sum(m.flat) # Print the sum print 'Sum of values of', path, ' = ', sum ------- > Date: Wed, 12 Apr 2006 14:46:14 -0700 > From: Eran Shacham <eshacham(a)burnham.org> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: Sum of volume data values > > Hey Tom, > > Thanks for your reply. However, I would like to do that from within a > script I already wrote. i.e I would like to integrate a read_in method > for an MRC file, access it values and then calculate the sum. I would > like to avoid doing that by opening my file in Chimera at this stage of > the program. Can it be done by importing some of your code? > > Thanks, > Eran.

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