- Chimera-users - RBVI Mailing Lists

Stereo on the 1.2304 version
by Anna Feldman-Salit 28 Nov '06

28 Nov '06

Hello, Unfortunately, I'm facing with a problem of stereo option on the version 1.2304. I can see the stereo when I turn the "stereo" option on, but the quality of the picture is not of the best ones. The main picture is likely screened on background, while it's also impossible to focus on the frontal part. I was playing a bit with camera-viewing parameters, but nothing worked for me. Before, working with pymol I used the "swap sides" option, which helped a lot. I tested our stereo glasses with pymol's stereo option again and it works smoothly. Since I definitely prefer to work with chimera, I would appreciate if this problem would be solved somehow. Do you have any suggestions? Thank you in advance! Best, Anna

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Re: [Chimera-users] Increase/decrease the sphere
by Eric Pettersen 28 Nov '06

28 Nov '06

I forgot to mention that if you want to control ball/stick size on a more permanent basis, you can use the New Molecule preferences (Favorites->Preferences) to set them for all new molecules you open. --Eric On Nov 27, 2006, at 9:21 PM, tuhin(a)iitk.ac.in wrote: > Thanks for your helpful suggestion, Eric. > > Regards, > TKP > >> Hi, >> Sphere size is the same as the atom's VDW radius. You can change >> atom radii with the "vdwdefine" command, or by selecting atoms and >> bringing up the Selection Inspector (click on the button at the lower >> right of the Chimera interface) and typing a new value into the >> "radius:" field. >> Ball and stick size are controlled on a per-model basis. Use the >> Model Panel (Favorites->Model Panel) and double-click on line with >> the model you want to control. A dialog listing the attributes of >> that model will come up. The "ball scale:" field controls the size >> of balls. It is a fraction that the VDW radius is multiplied by to >> get the ball size (default: 0.25). The "stick scale:" field controls >> stick size and also a fraction that sticks get multiplied by. The >> default stick radius is 0.2 angstroms and default stick scale is 1.0, >> so the final default radius is 0.2 angstroms. The help page for the >> attribute dialog describes why there are two numbers involved if you >> care, and also describes the other attributes if you're interested. >> >> --Eric >> Eric Pettersen >> UCSF Computer Graphics Lab >> pett(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu >> >> >> On Nov 27, 2006, at 6:56 AM, tuhin(a)iitk.ac.in wrote: >> >>> Dear Chimera users, >>> >>> Could anybody tell me whether there is a way in chimera to >>> increase/decrease the size of the spheres/ball-and-stick in atom >>> display >>> (Action-->Atoms/Bonds-->sphere...). The wireframe has an option in >>> "wire >>> width", is there something like that for the above two options ?? >>> >>> Waiting for yours suggestions. >>> Thanks in advance. >>> >>> Best, >>> TKP >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >

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Control of the volume viewer from the command line
by Lukas Palatinus 28 Nov '06

28 Nov '06

Hello all, I am trying to make a movie showing an evolution of an electron density map during an iterative optimization. For each optimization step I have one density map as volume data in xplor format. I depict the maps using the volume viewer, where I can set the number and level of the isosurface thresholds as well as their color. However, each newly opened map opens with default threshold setting, which is not suitable for my purposes. I make the movie using a command file of the type: open density1.xplor movie record wait 10 movie stop close 0 open density2.xplor movie record wait 10 movie stop ... I would need to be able to control the properties of the isosurfaces of the newly opened map from the command line or from the script file, or find a way to preserve the properties set for the first map in all subsequently opened maps. The search in Chimera manual did not lead me anywhere. Could anyone give me a hint how to proceed? With best regards Lukas Lukas Palatinus Laboratoire de Cristallographie EPFL Lausanne Tel.: +41 (0)21 693 0639 mailto: palat(a)fzu.cz

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Re: [Chimera-users] Get angles in degree out of Rotation matrix
by Thomas Goddard 27 Nov '06

27 Nov '06

Hi Michael, Perhaps you can compare the orientation between the exact symmetric placement of a chain and the actual position by measuring the translation and rotation angle needed to align the two. By rotation angle I mean that any rotation can be represented as a rotation about a single axis (which depends on the rotation). I do not understand what you mean by rotation angles about x, y and z axes. As I mentioned that depends on the order of the rotations and therefore is rarely used. In the Chimera match command or matchmaker tool the optimal rotation matrix is computed -- it is *not* decomposed into separate x, y and z rotations during that calculation. I suppose if your system has symmetry about the z axis you could ask what rotation about z best aligns a chain with the exact symmetric chain location. In other words, only a z-axis rotation rather then rotation about an arbitrary axis would be allowed. Chimera does not have code for that and I have never heard that number reported. If you spell out precisely what angle is needed I can give better advice on how to get it from Chimera. Tom > From: "Stohr, Michael" <stohr(a)uni-mainz.de> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Date: Mon, 27 Nov 2006 09:51:31 +0100 > Subject: AW: Get angles in degree out of Rotation matrix > > Hi Tom, > > Thanks a lot for your description. It does not fit completely my demand. I will rephrase my question, is there a simple way to determine the three angles between the two 3d-structures of two identical chains? The background is that my molecule is not absolutely symmetrical and I want to quantify the asymmetry. So, I want to be able to say, this angle between this two chains differs from ideal symmetry angle by X degrees for different directions (x, y, z). I thought the rotation matrix would be the way to do so, but it does not seem so. I've found a not very precise method by using the distance tool and trigonometric functions. Therefore, if there is no answer for my question it will be ok at first especially I have to finish my theses very soon. By the way, in which order does for example the tool match or matchmaker rotates a structure or is this not predictable? > > Thanks for your afford, > Michael

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Increase/decrease the sphere
by tuhin＠iitk.ac.in 27 Nov '06

27 Nov '06

Dear Chimera users, Could anybody tell me whether there is a way in chimera to increase/decrease the size of the spheres/ball-and-stick in atom display (Action-->Atoms/Bonds-->sphere...). The wireframe has an option in "wire width", is there something like that for the above two options ?? Waiting for yours suggestions. Thanks in advance. Best, TKP

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Re: [Chimera-users] DelPhi
by Elaine Meng 24 Nov '06

24 Nov '06

Hi Stefano, Oh I see - it appears to be a problem with the Mac DelPhi download. I tried getting this myself, and could not run the executable, with this error message (probably the same problem you had): meng% /Users/meng/Desktop/release1.1/exe/delphiMacOSX; exit dyld: /Users/meng/Desktop/release1.1/exe/delphiMacOSX can't open library: /opt/ibmcmp/lib/libxlf90.dylib (No such file or directory, errno = 2) Trace/BPT trap logout [Process completed] I'm not an expert at understanding these messages, but it looks like the executable is looking for some code library that is not there. If you could run the executable successfully, the next step would be to put it in your "path," so that just typing the name of the executable in a Mac Terminal window would run the program. That would allow DelPhiController to connect properly. You would also want to download the DelPhi "sample data" http://luna.bioc.columbia.edu/honiglab/software/DelPhi/data.tar.gz which has charge and radius parameter files that can be used with the program. Sadly, in our current situation, we cannot use the program. I do not have the programming expertise to fix this library problem, but if any of us figures it out, we will definitely let you know. If you do get a fix from the Honig lab, it would be great if you could let me (or chimera-users) know - probably several of us would like to use this software on a Mac. Sorry about the trouble, Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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DelPhi
by Stefano Ciurli 24 Nov '06

24 Nov '06

Hello, does anyone know how to implement the DelPhi algorithm into Chimera? I am using a Powerbook G4. Thanks a lot Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

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fitting map into map
by Gabor Papai 24 Nov '06

24 Nov '06

Hi, Does anybody know if there is a way to calculate fitting of EM density map into another EM density map? I know how it goes with PDBs, but couldn't figure out how I can do it with maps. Thanks for help in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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question about using swapaa in Chimera
by Ng, David (NIH/NCI) [E] 22 Nov '06

22 Nov '06

Hi, I'm currently learning to use Chimera. I wish to look at specific amino acid mutations in CDKN2A for effects in conformational changes and changes in protein interactions with known partners. When I type the command "swapaa P #0:24" in chimera to mutate arginine 24 to proline in CDKN2A, I get an error message that says "Value error: No connectivity template for residue P" Can you help me with this issue? Thanks. David Ng, M.D. Staff Clinician

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Re: [Chimera-users] Get angles in degree out of Rotation matrix
by Thomas Goddard 20 Nov '06

20 Nov '06

Hi Michael, It is not very common to specify a 3-dimensional rotation in terms of a x-axis rotation, y-axis rotation and z-axis rotation because this decomposition depends on the order of the x, y, and z rotations. If you rotate 90 degrees about the x-axis, then 90 about the y-axis you get a different orientation than if you do the y-axis rotation first followed by the x-axis rotation. Chimera has a routine to produce the rotation axis (a unit vector in 3-dimensions) and rotation angle about that vector corresponding to a 3x3 rotation matrix. You could use that in Chimera with some Python code. If you just want the rotation angle and don't need the axis then the formula is simple Tr(R) = 1 + 2*cos(theta) where Tr(R) = sum of rotation matrix diagonal elements so the rotation angle theta = arccos((Tr(R) - 1)/2) Below I give the Chimera C++ code that also computes the axis. There are corner cases handled by this code for 0 degree and 180 degree rotations. Tom void Xform::getRotation(Vector *axis, Real *angle) const { Real cosTheta = (rot[0][0] + rot[1][1] + rot[2][2] - 1) / 2; if (fuzzyEqual(cosTheta, 1)) { *angle = 0; (*axis)[0] = (*axis)[1] = 0; (*axis)[2] = 1; return; } if (!fuzzyEqual(cosTheta, -1)) { *angle = degrees(acos(cosTheta)); Real sinTheta = sqrt(1 - cosTheta * cosTheta); (*axis)[0] = (rot[2][1] - rot[1][2]) / 2 / sinTheta; (*axis)[1] = (rot[0][2] - rot[2][0]) / 2 / sinTheta; (*axis)[2] = (rot[1][0] - rot[0][1]) / 2 / sinTheta; return; } *angle = 180; if (rot[0][0] >= rot[1][1]) { if (rot[0][0] >= rot[2][2]) { // rot00 is maximal diagonal term (*axis)[0] = sqrt(rot[0][0] - rot[1][1] - rot[2][2] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[0]); (*axis)[1] = halfInverse * rot[0][1]; (*axis)[2] = halfInverse * rot[0][2]; } else { // rot22 is maximal diagonal term (*axis)[2] = sqrt(rot[2][2] - rot[0][0] - rot[1][1] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[2]); (*axis)[0] = halfInverse * rot[0][2]; (*axis)[1] = halfInverse * rot[1][2]; } } else { if (rot[1][1] >= rot[2][2]) { // rot11 is maximal diagonal term (*axis)[1] = sqrt(rot[1][1] - rot[0][0] - rot[2][2] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[1]); (*axis)[0] = halfInverse * rot[0][1]; (*axis)[2] = halfInverse * rot[1][2]; } else { // rot22 is maximal diagonal term (*axis)[2] = sqrt(rot[2][2] - rot[0][0] - rot[1][1] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[2]); (*axis)[0] = halfInverse * rot[0][2]; (*axis)[1] = halfInverse * rot[1][2]; } } }

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Re: [Chimera-users] suggestion
by Thomas Goddard 20 Nov '06

20 Nov '06

Hi David, Thanks for your suggestion to add coloring of isosurfaces based on gradient magnitude to Chimera. I think I can add this to the Surface Color tool in an hour or two since the gradient calculation code is already in Chimera (for fitting atomic models in maps). I'll try to put it in soon and send you the code to test. Description of coloring from article: "OpenDX (www.opendx.org) module MAKROVIS was implemented to create masks of different shapes and to analyze disorder in the reconstructions (Figure 1B). For this, isosurface rendering of a given voxel was colored as a function of the maximum density difference between the voxel and its neighbors." Tom > From: "David G. Morgan" <dmorgan(a)ucdavis.edu> > To: goddard(a)cgl.ucsf.edu > Subject: suggestion > Date: Thu, 16 Nov 2006 19:03:50 -0800 > > Tom, > > I have a suggestion for the developers "list of ideas to implement," if > you think there would be enough interest from users and that it is > something that chimera should do. I realize that you get lots of > suggestions, and that some of them are simply outside the realm of what > the chimera developers think chimera is intended to do. But since you > do ask for suggestions, here's my most recent one. > > I'm attaching a recent journal article where the authors used a color > coding scheme to display "order/disorder" regions of an EM > reconstruction. The images are in Fig 1 B and the rather sparse > description of the "algorithm" is a single sentence in the "Image > Processing 3D Reconstruction" section (p 1046). The idea of color > coding some estimate of the better defined regions of a density map is > very nice (and clever), and would be extremely helpful in lots of > situations (my plug for wanting you guys to implement something > similar...). > > The idea behind this is that for any given region of iso-surface, the > density gradient normal to that surface should be a reasonable measure > of how well defined the density is. In other words, a very steep > gradient (e.g., a fast transition between protein and solvent) means > very well defined density and a flat gradient means weakly defined > density (disordered regions, partial occupancy, etc.). The authors > don't do such a complicated calculation, but it seems that what they > implemented at least captures most of this sort of character. > > I think the key to this is that the gradient is calculated "locally." > I've looked at gradients as a function of resolution with the idea of > using it to help chose a proper iso-surface. While it works well with > model data, real reconstructions aren't nearly so well behaved. I > hadn't thought about this in a while, but I think what the authors have > done both helps explain the behavior of my real data (the gradient is > simply too varied) and is a quite useful visualization tool. > > So please think about implementing something like this in the volume > handling tools of chimera. > > David Gene Morgan > Advanced Microscopy & Proteomics > Molecular & Cellular Biology > University of California at Davis > 530 752 2693 (lab) > 530 752 3085 (FAX) > ---- > removed PDF for > > Huiskonen JT, de Haas F, Bubeck D, Bamford DH, Fuller SD, Butcher SJ. > Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging. > Structure. 2006 Jun;14(6):1039-48.

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Duplicate Atom Serial Numbers
by Albion Baucom 17 Nov '06

17 Nov '06

When I generate a PDB file, and generate symmetry related biological units, I frequently replicate the single structure. When I do this the atoms numbers get duplicated and when I open the structure in Chimera it prints to the screen warning: duplicate atom serial number found: NNNN where NNNN is the duplicate number. The problem with this is it slows down opening the file by a huge factor. I assume that the print statement to the terminal is adding a lot of time to the file reading process. Is there any way around this, or a way to simply turn this off? I am not concerned with the specifics of the duplicate atom numbers. A single error message to alert me the fact that there are duplicate atoms would be enough. Once Chimera is done reading the structure it works fine. Rotations are smooth. Displaying ribbons is quick, etc. This doesn't appear to be a slow down due to atom limitations, but simply the overhead of printing that error message over and over to the console. Of course I am aware that there are BIOMT records to generate symmetry related molecules using a single repeating unit, or I could generate separate PDB files for each repeating unit, but this is a lot more work and bookkeeping when I can use some existing simple programs to simply rotate and translate a single set of coordinates. Thanks Albion

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deleting model memories
by wendy ochoa 15 Nov '06

15 Nov '06

Is there a way to delete model memories in the emanimator option? thanks a lot wendy

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Question about molecular surface generation
by Nihshanka Debroy 15 Nov '06

15 Nov '06

Hi Chimera users, I have been generating molecular surfaces for several proteins and am hoping to perform some matrix calculations on the points where the surfaces are being calculated. So I was wondering if there is a way to reduce the # points where the surface is calculated/plotted, as that would really reduce the dimensions of my matrices! I am using the Delphi Controller to generate electrostatic potentials. My understanding of Delphi is that it finds finite difference solutions to the Poisson Boltzmann equation by mapping the system onto a grid of points. After the potentials are calculated at those grid points, when generating the potentials on the molecular surface, interpolation is used to calculate the potentials for locations on the molecular surface that are between points on the grid used in Delphi. So I don't think its the grid size for Delphi that I need to be reducing, but the # points where the actual molecular surface is calculated. Is it possible to reduce this number somewhere in the code files? Thanks a lot! Sincerely, Nihshanka

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MultiAlign viewer
by Mireille Krier 14 Nov '06

14 Nov '06

Dear all, I want to add to the header of a sequence alignment graphical representations such as cylinders and thick arrows to symbolize stretches of helix and strand. Is this possible? Should one annotate this in the Stockholm format file (and if yes could you provide me an example file) ? Cheers, Mireille

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About electrostatic potentials
by xiaobinfan＠tju.edu.cn 14 Nov '06

14 Nov '06

Dear Sir/Madam: Thank you for reading. I am a new Chimera's user in China. I wonder whether the surface of a virus opened by Chimera could be colored by its electrostatic potentials calculated by the DelPhiController. I can color the surface of a small protein on Linux platform now. However, the surface of a whole virus (PDB 1ny7) opened by the Multiscale Models could not. Does it possible to do that? Thank you for your support. Best wishes! Sincerely, Xiaobin Fan ---------------------------

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Fwd: longbond and session restore problems
by Elaine Meng 14 Nov '06

14 Nov '06

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: November 14, 2006 10:36:35 AM PST > To: jean-francois menetret <menetret(a)bu.edu> > Cc: Eric Pettersen <pett(a)cgl.ucsf.edu>, Thomas Goddard > <goddard(a)cgl.ucsf.edu>, Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] longbond and session restore problems > > Hi Jean-Francois, > In my tests I didn't have this problem; showing Pipes-and-Planks > should not change which atoms and bonds are shown. > > However, I might understand what is happening: when you show the > "chain trace" of CA atoms only, a connection across the missing > part is shown even after you use "~longbond". This CA connection > line is different than the "missing segments" pseudobonds: > > -CA-CA-------CA-CA- > is the chain trace, not affected by ~longbond > > -N-CA-C- - - -N-CA-C- > is the backbone showing "real bonds" except for the pseudobond, > which is affected by ~longbond > > If you are showing just the CA atoms and you don't want the > connection, here are some possibilities: > (1) just hide all the CA atoms (for example, command: ~disp @ca) > OR > (2) change from "chain trace" (the CA atoms) to "backbone > only" (N,CA,C) - if you used ~longbond the connection will be gone > OR > (3) if you really wanted to keep showing just the CA atoms, you can > select each long CA-CA bond (which is also a pseudobond, although > not shown with a dashed line) with Ctrl-click, and use the > Selection Inspector to undisplay it. This tool is opened by > clicking the button on the lower right of the Chimera window. In > the Inspector, change to Inspect [Pseudobond] and change the > "displayed" attribute to "false." > > I hope this helps, > Elaine > > On Nov 14, 2006, at 6:51 AM, jean-francois menetret wrote: > >> Hi Elaine, >> >> thank you for your message >> I still have one problem with the long bonds, though : there >> reappear in pipes-and-plancks. >> About restoring a session, I agree, it was not an issue with the >> chimera version but with the speed/memory of my PC. Although >> chimera could save the session, it couldn't reopen it on my PC but >> it did on a faster one. >> >> Best wishes >> >> Jean-François Ménétret, PhD >> Boston University School of Medicine >> Physiology and Biophysics Department >> 700 Albany Street W315 >> Boston, MA 02118 >> Email: menetret(a)bu.edu >> Mailing address: 715 Albany Street > > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html >

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longbond and session restore problems
by Thomas Goddard 09 Nov '06

09 Nov '06

Here are two problems reported by Jean-Francois Menetret in Chimera 2304 and 2306. ------- Start of forwarded message ------- Date: Thu, 9 Nov 2006 16:38:58 -0500 (EST) From: jean-francois menetret <menetret(a)bu.edu> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: problems report Hi Thomas, I have two problems to report 1) the longbond command doesn't seem to work (with chimera 2304 or 2306) 2) I saved a session under chimera 2304 but couldn't open it after=20 upgrading to 2306 Jean-Francois Jean-Fran=E7ois M=E9n=E9tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street ------- End of forwarded message -------

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Re: [Chimera-users] Fwd: Chimera crashes with MacPro show solid
by Thomas Goddard 09 Nov '06

09 Nov '06

Peter EngelHardt replies about solid rendering crash on Mac. ------- Start of forwarded message ------- Date: Thu, 9 Nov 2006 22:42:41 +0300 To: Thomas Goddard <goddard(a)cgl.ucsf.edu> From: Peter Engelhardt <engelhar(a)medi.mappi.helsinki.fi> Subject: Re: [Chimera-users] Fwd: Chimera crashes with MacPro show solid Dear Tom, Thanks, I did what you told and it all worked out very fine Though a bit buggy - volumes disappear and appear suddenly - but under certain control anyhow. Cheers and thanks again Peter > The crash with solid rendering is almost surely a graphics driver bug. >The solid rendering code works correctly on many different graphics cards >and there is nothing in that code that works differently for stereo >rendering. > > Does the crash occur for solid rendering without stereo? yes instantly > > Does the size of the data set matter? not tested > > There are two solid rendering options that may avoid this crash. >These are shown in the volume dialog using the Features / Solid Rendering >Options menu entry. From the back trace you sent I see the crash occurs >when pushing the data to the graphics card and mapping the colors using >a colormap. If you turn off the option "Use colormap of size X for solids" >then different code will be used -- colors will be computed on the CPU >instead of on the graphics card. A second change that may avoid the >crash is turning off "Solids using 2D textures". This makes Chimera use >3 dimensional textures instead of 2 dimensional textures. > > Tom - -- ___________________________________________________________ Peter Engelhardt, PhD, docent Assistant Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology and Virology Haartman Institute P.O.Box 21, FI-00014 Univ. of Helsinki, Finland Visiting Address: Haartmaninkatu 3, Helsinki ------- End of forwarded message -------

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Fwd: Chimera crashes with MacPro show solid
by Peter Engelhardt 09 Nov '06

09 Nov '06

In our Mac Pro Quad-Core 2.66GHz CTO Processor: 2.66 GHz Quad Xeon RAM 4G and NVIDIA Quadro FX 4500 512MB SDRAM, using Crystal Eyes Stereo Stereo works with iso surface and mesh but: CRASHES with show solid? Peter PS Following errors were reported and fwd to apple. >Date/Time: 2006-11-07 17:17:49.047 +0200 >OS Version: 10.4.8 (Build 8L2127) >Report Version: 4 > >Command: python2.4 >Path: /Applications/Chimera.app/Contents/Resources/bin/python2.4 >Parent: WindowServer [55] > >Version: 1.2303 (1.2303) > >PID: 457 >Thread: 0 > >Exception: EXC_BAD_ACCESS (0x0001) >Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x000000a4 > >Thread 0 Crashed: >0 libGLImage.dylib 0x940a3fc4 glgProcessColor(GLDPixelMode >const*, GLGOperation const*, unsigned long) + 46870 >1 libGLImage.dylib 0x940972aa glgProcessPixels + 296 >2 com.apple.GeForceFXGLDriver 0x028b4f1e gldGetTextureLevel + 10243 >3 GLEngine 0x02732062 glTexSubImage2D_Exec + 1633 >4 libGL.dylib 0x92b0edaa glTexSubImage2D + 139 >5 _volume.so 0x037fb30f Texture_2d::fill(unsigned >short*) + 147 >6 _volume.so > 0x037fb424 Texture_Plane::fill_texture() >+ 76 >7 _volume.so 0x037fb627 >Volume_Renderer_2DT::update_colormap_textures(int) + 159 >8 _volume.so 0x037fd865 >Volume_Renderer_2DT::update_texture_planes(int) + 567 >9 _volume.so > 0x037fd9d8 Volume_Renderer_2DT::draw() + >122 >10 _chimera.dylib > 0x0101c5f8 chimera::LensModel::xformDraw >(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const + 572 >11 _chimera.dylib 0x010190e1 chimera::Lens::draw >(chimera::LensViewer const*, chimera::LensViewer::DrawPass, int const*) + >241 >12 _chimera.dylib 0x01020e98 >chimera::LensViewer::drawScreenBoxes(otf::Array<int, (unsigned long)4> >const&, __gnu_cxx::__normal_iterator<chimera::ScreenBox*, >std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >, >__gnu_cxx::__normal_iterator<chimera::ScreenBox*, >std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >) >const + 1024 >13 _chimera.dylib 0x01022674 chimera::LensViewer::draw >(bool) const + 460 >14 _chimera.dylib > 0x0101dd34 chimera::LensViewer::displayCB >(_object*) + 90 >15 _chimera.dylib 0x01095323 LensViewer_displayCB + 43 >16 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >17 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >18 python2.4 0x000b89dc builtin_apply + 201 >(bltinmodule.c:100) >19 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >20 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >21 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >22 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >23 python2.4 0x0000c662 instancemethod_call + 401 >(classobject.c:2447) >24 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >25 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >26 _tkinter.so 0x016efea4 PythonCmd + 220 (_tkinter.c: >2001) >27 libtcl8.4.dylib 0x0a00d10f TclInvokeStringCommand + 121 >28 libtcl8.4.dylib 0x0a00fa41 TclEvalObjvInternal + 769 >29 libtcl8.4.dylib 0x0a010694 Tcl_EvalObjv + 232 >30 libTogl2.0.dylib 0x0255d047 Togl_CallCallback + 144 >31 libTogl2.0.dylib 0x0255d235 Togl_Render + 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>Versions/A/Resources/libTIFF.dylib >0x91bac000 - 0x91bc6fff libPng.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libPng.dylib >0x91bcb000 - 0x91bcdfff libRadiance.dylib > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib >0x91bcf000 - 0x91bcffff com.apple.Accelerate 1.3.1 (Accelerate 1.3.1) > /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate >0x91bd1000 - 0x91c5ffff com.apple.vImage 2.5 > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ >vImage.framework/Versions/A/vImage >0x91c66000 - 0x91c66fff com.apple.Accelerate.vecLib 3.3.1 (vecLib 3.3.1) > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ >vecLib.framework/Versions/A/vecLib >0x91c68000 - 0x91cc1fff libvMisc.dylib /System/Library/Frameworks/ 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0x92b23fff libGL.dylib /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Libraries/libGL.dylib >0x92b2e000 - 0x92b86fff libGLU.dylib /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Libraries/libGLU.dylib >0x92b9a000 - 0x92b9afff com.apple.Carbon 10.4 (???) > /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon >0x92b9c000 - 0x92bacfff com.apple.ImageCapture 3.0.4 > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >ImageCapture.framework/Versions/A/ImageCapture >0x92bbb000 - 0x92bc3fff com.apple.speech.recognition.framework 3.6 > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >SpeechRecognition.framework/Versions/A/SpeechRecognition >0x92bc9000 - 0x92bcffff com.apple.securityhi 2.0.1 (24742) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >SecurityHI.framework/Versions/A/SecurityHI >0x92bd5000 - 0x92c66fff com.apple.ink.framework 101.2.1 (71) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >Ink.framework/Versions/A/Ink >0x92c7a000 - 0x92c7efff com.apple.help 1.0.3 (32.1) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >Help.framework/Versions/A/Help >0x92c81000 - 0x92c9ffff com.apple.openscripting 1.2.5 (???) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >OpenScripting.framework/Versions/A/OpenScripting >0x92cb1000 - 0x92cb7fff com.apple.print.framework.Print 5.2 (192.4) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >Print.framework/Versions/A/Print >0x92cbd000 - 0x92d20fff com.apple.htmlrendering 66.1 (1.1.3) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >HTMLRendering.framework/Versions/A/HTMLRendering >0x92d47000 - 0x92d88fff com.apple.NavigationServices 3.4.4 (3.4.3) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >NavigationServices.framework/Versions/A/NavigationServices >0x92daf000 - 0x92dbdfff com.apple.audio.SoundManager 3.9.1 > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >CarbonSound.framework/Versions/A/CarbonSound >0x92dc4000 - 0x92dc9fff com.apple.CommonPanels 1.2.3 (73) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >CommonPanels.framework/Versions/A/CommonPanels >0x92dce000 - 0x930c2fff com.apple.HIToolbox 1.4.8 (???) > /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ >HIToolbox.framework/Versions/A/HIToolbox >0x931c8000 - 0x931d3fff com.apple.opengl 1.4.12 > /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL >0x94096000 - 0x940d0fff libGLImage.dylib /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Libraries/libGLImage.dylib >0x9492b000 - 0x94950fff libssl.0.9.7.dylib > /usr/lib/libssl.0.9.7.dylib >0x96451000 - 0x96451fff com.apple.vecLib 3.3.1 (vecLib 3.3.1) > /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib >0x969cb000 - 0x96a99fff libGLProgrammability.dylib > /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/ >libGLProgrammability.dylib >0x96ab4000 - 0x96ab5fff libGLSystem.dylib > /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/ >libGLSystem.dylib >0x99756000 - 0x99762fff libXplugin.1.dylib > /usr/lib/libXplugin.1.dylib > >Model: MacPro1,1, BootROM MP11.005C.B01, 4 processors, Dual-Core Intel Xeon, >2.66 GHz, 5 GB >Graphics: NVIDIA Quadro FX 4500, NVIDIA Quadro FX 4500, PCIe, 512 MB >Memory Module: DIMM Riser A/DIMM 1, 512 MB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser A/DIMM 2, 512 MB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser B/DIMM 1, 1 GB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser B/DIMM 2, 1 GB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser A/DIMM 3, 1 GB, DDR2 FB-DIMM, 667 MHz >Memory Module: DIMM Riser A/DIMM 4, 1 GB, DDR2 FB-DIMM, 667 MHz >Network Service: Built-in Ethernet 1, Ethernet, en0 >PCI Card: NVIDIA Quadro FX 4500, Display, Slot-1 >Serial ATA Device: ST3250824AS P, 232.89 GB >Parallel ATA Device: SONY DVD RW DW-D150A >USB Device: Hub in Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, >500 mA >USB Device: Apple Optical USB Mouse, Primax Electronics, Up to 1.5 Mb/sec, >100 mA >USB Device: Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, 250 mA >FireWire Device: built-in_hub, unknown_value, Unknown > > >___________________________________________________________ >Peter Engelhardt, PhD, docent >Assistant Professor in Molecular Genetics >Unit of Molecular Electron Tomography >Department of Pathology and Virology >Haartman Institute >P.O.Box 21, FIN-00014 Univ. of Helsinki, Finland >Visiting Address: Haartmaninkatu 3, Helsinki >Office Tel: (+358-9)-19126431 (direct) >Laboratory Tel: (+358-9)-19126441 >EM-facilities, Tel: (+358-9)-19126885 >Digiroom: Tel: (+358-9)-1912886 >Fax: (+358-9)-19126491 >FIN-00014 Univ. of Helsinki, Helsinki, Finland > >LCE, Laboratory of Computational Engineering, >Research Center for Computational Science and Engineering >Helsinki University of Technology (HUT), >P.O.Box 9203, FIN-02015 HUT, FINLAND >Visiting Address: Innopolis2, Tekniikantie 14, Espoo > >Home address: > Lindstedstvägen 1 B 7 > FIN-02700 Grankulla, > Finland >Tel: (+358-9)-5091381 > > Mobil Phone: +358 (0)415610171 > Email: Peter.Engelhardt(a)Helsinki.Fi > URL: http://www.lce.hut.fi/~engelhar/ -- ___________________________________________________________ Peter Engelhardt, PhD, docent Assistant Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology and Virology Haartman Institute P.O.Box 21, FI-00014 Univ. of Helsinki, Finland Visiting Address: Haartmaninkatu 3, Helsinki Office Tel: (+358-9)-19126431 (direct) Laboratory Tel: (+358-9)-19126729, 19126442 EM-facilities, Tel: (+358-9)-19126885 Fax: (+358-9)-19126700 Laboratory of Computational Engineering, Research Center for Computational Science and Engineering Helsinki University of Technology (HUT), P.O.Box 9203, FI-02015 HUT, FINLAND Visiting Address: Innopolis2, Tekniikantie 14, Espoo Office Tel: (+358-9)-4514843 (direct) Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: (+358-9)-5091381 Mobile Phone: +358-(0)41 561 0171 Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/

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queries on making image
by bala 09 Nov '06

09 Nov '06

Hello chimera users, 1) I hve to show two molecules in the same figure side by side. When i am displaying, i have a problem that both molecules are not coming at same plane. Is there any option to adjust this. 2) I labelled both these molecules. The labels are coming fine in the screen. But when i create an image (i save it as tif file), some labels are getting hided below my molecular surface. Which option i should use to rectify that. 3) How one can add text on the screen/near a particular spot on the molecule ? 4) Someone kindly Suggest me on best settings (i mean values) of the resolution based on your experience of making figures using chimera or which you normally use. Thanks in advance, Bala

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Re: [Chimera-users] font change in v1.2303+
by Sabuj Pattanayek 07 Nov '06

07 Nov '06

Hi, Yes, now that you mention it I think we have confused each other. I am talking about the fonts in the widgets and dialogs and not the annotation fonts in the linux version. I will grab an old install from http://www.cgl.ucsf.edu/chimera/olddownload.html, and make a screenshot comparing that with the latest 1.2304. I don't think I saw this change in the WinXP version, but I'll check that too. Thanks, Sabuj Elaine Meng wrote: > Hi Sabuj, > It seems like Greg's response was about the labels on the structures, > whereas you said "gui" which I interpret as the widgets and dialogs. > Were you asking about these? I noticed that the font for the "Really > Exit?" dialog is now different, but I haven't seen differences in other > dialogs. > Elaine

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sparky-chimera error
by ksgodin＠u.washington.edu 07 Nov '06

07 Nov '06

Hi all, I having been trying to open an ensemble of NMR structures with the 'km' feature of Sparky. Everything opens fine, but the Model Panel does not open properly. The error log sites Program Files\Sparky\python\lib-tk\Tix.py, line 477, in_init_ self.stylename=self.tk.call ('tixDisplayStyle', itemtype, TclError: invalid command name "tixDisplayStyle" Does anyone know how to fix this? It comes up with Sparky 3.111 and Chimera 1.2065 or 1.1195. Thanks, Kate ~~~~~~~~~~~~~~~~~~~~~~ Kate Godin UW Chemistry Dept Varani Group BAG 63 ~~~~~~~~~~~~~~~~~~~~~~

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font change in v1.2303+
by Sabuj Pattanayek 04 Nov '06

04 Nov '06

Hi, The gui font seems to have changed in v1.2303+ . Is there some way to change it back to the old font? Thanks, Sabuj

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stereo
by hsosa＠aecom.yu.edu 03 Nov '06

03 Nov '06

How can I use stereo (sequential mode) ?. If I click the stereo button in the camera dialog or start chimera using the command chimera --stereo. I get the error message: Unable to turn on stereo viewing Unable to find hardware stereo support (coulddm't choose stereo pixel format Couldn't figure togl widget) My graphic cards is a NVIDIA Quadro4 900 XGL. The Nvdia Stereo driver (v: 91.31) is installed and enabled. Chimera version is: 1 build 2255 2006/06/23 Monitors: Two (dual) digital DELL 1900 FP Computer: Dual Xeon 1.4 Ghz, 1GB of RAM. Running Windows XP Thanks Hernando --

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