- Chimera-users - RBVI Mailing Lists

Delphi Controller
by sette＠uniroma2.it 11 Dec '06

11 Dec '06

Dear all, I have a simple question: does Delphi controller works under unix only or it is possible to work with it under Linux and/or Windows XP? Thanks a lot, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

5 4

Read compressed PDB files -question, suggestion
by Moo Cow 08 Dec '06

08 Dec '06

We store the PDB locally, but compressed. Can one persuade chimera to read coordinates from a pipe ? Maybe this could be done at the python level. It might also not be too hard to use the python binding to the zlib library, but I would not know how to do this. I imagine the interest (or not) would not be limited to reading PDB files. many thanks for any suggestions. -- Search for products and services at: http://search.mail.com

3 2

Apply the symmetry to the fitted models in map
by Hong-Wei Wang 06 Dec '06

06 Dec '06

Hi, Tom I remember you were showing docking a model into map with high symmetry (you showed the actomyosin filament example). I am wondering how you generate the symmetry in the docking and if the symmetry information is necessary for the correct fitting. Thanks a lot! Hongwei ----------------------------------- Hongwei Wang, Ph D MS 20A-355, LSD, LBNL 1 Cyclotron Rd, Berkeley, CA 94720 510-642-2222 (O) 510-642-8806 (FAX) hwwang(a)lbl.gov

2 1

volume viewer issue
by Matthew Shawkey 06 Dec '06

06 Dec '06

Hi, I am using chimera to visualize a stack of EM serial sections. I can load them into Chimera (as MRC file), but when I try to view the stack in the volume viewer w the "solids" option all I see is a white square.. w the mesh and surface options the stack shows up as a grainy image on which it's difficult to see any depth.. any suggestions? THanks, Matt

2 1

Uploading several trajectories for MDmovie
by Anna Feldman-Salit 04 Dec '06

04 Dec '06

Dear all, I would like to know if there is any possibility to sequentially upload several trajectories with MDmovie option (or command line) and then to visualize them with "no stop" in between. These trajectories were generated by AMBER with "restart" input files. Such an option happens to be in VMD, but it's more convenient for me to work with Chimera (I have Chimera1.2304). Thanks a lot in advance, Anna

2 1

Fit models to map
by hsosa＠aecom.yu.edu 04 Dec '06

04 Dec '06

I wonder how the "Fit models to map" function do the fitting. Does it find the best cross-correlation value between a 3D density calculated from the atomic model and the 3D density map?. What is the maximum displacements and rotations tested around the current position? What is the step size of the rotations/displacements? Thanks Regards Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

2 1

Re: [Chimera-users] inter-surface calculations in Chimera
by Elaine Meng 01 Dec '06

01 Dec '06

Hi Gali, Eric forwarded your question to me. The Intersurf tool generates a surface between the interacting molecules that is different from the surface of either molecule - it is mainly useful for viewing an interface and showing its properties (for example, with coloring by hydrophobicity or electrostatic potential), but not for measuring the surface area. It is possible to measure volume and surface area in Chimera, but currently it is a long process. We hope to have a simpler process available in the future. I'll describe two different approaches. (1) the simpler and more approximate way to calculate buried surface area and void volume in the complex: approx buried surface area = [(surface area of X) + (surface area of Y) - (surface area of XY)] / 2 approx interface void volume = (volume of XY) - (volume of X) - (volume of Y) The "Measure Volume and Area" tool can be used to calculate the surface areas and volumes. [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/ measurevol.html ] The trick is to first make a surface that encloses both X and Y and measure its values. Then, make surfaces that separately enclose X and Y and measure again. Here is a concrete example. PDB structure 1cf7 has two protein chains A and B, two DNA chains C and D, and some water. I'd open the structure and delete everything but the protein and DNA. command: open 1cf7 command: select :.a-d command: sel invert command: delete sel command: surfcat complex :.a-d command: surf complex Tools... Surface/Binding Analysis... Measure Volume and Area (measure values for the complex) command: surfcat protein :.a-b command: surf protein (choose the protein surface in Measure Volume and Area, compute again) command: surfcat dna :.c-d command: surf dna (choose the dna surface in Measure Volume and Area, compute again) Finally, use the equations above. All the results can be viewed in the Reply Log (under Favorites). These values are for molecular surfaces (also known as solvent-excluded, where the probe touches), not solvent-accessible (traced by the probe center). For this structure, I calculate approx 530 square angstroms surface area buried, approx 730 cubic angstroms of interface void volume. (2) A more detailed approach can yield different values for the areas buried on X and Y: (surface area of X buried in the XY interface) = (surface area from all atoms of X in surface enclosing XY) - (surface area from all atoms of X in surface enclosing just X) with a similar equation for Y. Currently, the only way to get atomic rather than total surface areas in Chimera is by using the "Area/Volume from Web" tool [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html ] which uses a Web server at NCBI and loads the atomic values into Chimera. Because the MSMS option of the server has problems with nucleic acids, the only choice for your complexes is to calculate solvent-accessible surface areas (not the solvent-excluded surface areas calculated by method (1) above). The main trick is to first send only XY to the server (making sure solvent, ions, etc. are NOT included). Then using Attribute Calculator, [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html ] sum the values for the atoms of X in that combined surface, and likewise get a total for Y. Then, delete everything except X and send it to the server again, getting the total for X alone. Close/reopen the structure, delete everything except Y, and send it to the server to get the total for Y alone. Subtract the value for X (Y) in the complex from the total for X (Y) alone. Here is a concrete example. PDB structure 1cf7 has two protein chains A and B, two DNA chains C and D, and some water. I'd open the structure and delete everything but the protein and DNA. command: open 1cf7 command: select :.a-d command: sel invert command: delete sel Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the protein and DNA command: select :.a-b Tools... Structure Analysis... Attribute Calculator calculate an attribute (name doesn't matter) for "models" with the Formula: sum(atom.accessibleSurface) with the option "Restrict formula domain to current selection" write down the total for A-B (which is the PROTEIN IN THE COMPLEX) (I get approx 7473) command: select :.c-d calculate an attribute (name doesn't matter) for "models" with the Formula: sum(atom.accessibleSurface) with the option "Restrict formula domain to current selection" write down the total for C-D (which is the DNA IN THE COMPLEX) (I get approx 4502) command: delete :.c-d now only the protein is left Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the protein - get the total for PROTEIN ALONE (Favorites... Reply Log) (I get approx 8842) command: close 0 command: open 1cf7 command: select :.c-d command: sel invert command: delete sel now only the DNA is left Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the DNA - get the total for DNA ALONE (Favorites... Reply Log) (I get approx 5758) Use the equation above to get the buried solvent-accessible surface areas. I calculate approx 1369 square angstroms buried for the protein, approx 1256 square angstroms buried for the DNA. You can't compare these solvent-accessible areas to the solvent-excluded areas calculated by method (1) ... the solvent-accessible values are generally much larger. PHEW! I congratulate everyone who got this far. The written explanation makes it seem longer than actually performing the process. I hope this helps, Elaine On Nov 30, 2006, at 7:35 AM, galig wrote: > Dear Eric, > > I have a small question regarding the calculation of inter-surfaces in > Chimera: > I have several protein/DNA complexes, and I would like to compare > their protein/DNA interfaces. I used Tools-->surface/binding > analysis-->compute interface surface and chose the protein and DNA > chains. the result, if I understand it correct, is per atom. Is there > a place to find the overall number representing the contact surface? > is this a different or similar calculation? > One more thing- how do I calculate the void intermolecular volume > between the chains? > > Thank you and sorry to bother you, > > Gali Golan > Dept. of Inorganic Chemistry > The Hebrew U. of Jerusalem > Jerusalem 91904 Israel > Tel. 972-2-6585610 > Fax 972-2-6585319 > ----- 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

2 1

Re: [Chimera-users] Chimera on x86_64?
by Thomas Goddard 29 Nov '06

29 Nov '06

Hi Ben, There's no technical obstacle to us making regular 64-bit linux Chimera distributions. The only issue is having time to do it. The work involves compiling the ~30 third party libraries that Chimera uses. I did this is the past and it took about one day of fiddling. Our Chimera build scripts compile all of the third party libraries automatically and my past hand fiddling to build on 64-bit linux would have to be put into our scripts. That could take a 1 to 5 days of work. We have a 64-bit linux machine to do the work on. So it all comes down to when one of the 4 developers (Tom Goddard, Eric Pettersen, Greg Couch, or Conrad Huang) has time to work on that. I don't think I will have time until January at the earliest. Could you give me a better sense of how much need there is in the Sali lab? Are you really saying you would not install 32-bit Linux system libraries except for Chimera? I would think there are a fair number of applications out there with binary distributions only for 32-bit. The other problem you point out is that 32-bit Chimera Python cannot use your own 64-bit Python modules. Are you using additional C Python modules within Chimera that do not come with Chimera? That is interesting -- what are they? Tom > From: Ben Webb <ben(a)salilab.org> > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: Wed, 29 Nov 2006 12:51:27 -0800 > Subject: Chimera on x86_64? > > I wonder if you could give me a rough idea of when you plan to make > regular builds of Chimera on x86_64 (if at all)? All I've been able to > glean from the download page and the mailing list archive is that you > do make occasional builds, but recommend the 32-bit version. > > Memory isn't so much of an issue for us in particular (although we are > increasingly looking at large EM maps) but the requirement to have > 32-bit libraries is starting to become a problem. All of our new > desktops are x86_64 machines, and it's a pain to require the 32-bit > libraries just for Chimera. Additionally, our users want to > mix-and-match Python modules (including Modeller, of course) and > Chimera is unable to import any module which has a C backend, since > they're compiled for x86_64 and the Python interpreter in Chimera is > 32-bit. (Of course, we could recompile all of our other Python modules > for 32-bit, but that would cause problems with x86_64 apps.) > > If you need people to test x86_64 Chimera builds, we certainly have > some demanding users here to break them. ;) > > Ben > -- > ben(a)salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle

2 1

Multiple Volume Viewer Windows and saving PDB file
by Batsal Devkota 28 Nov '06

28 Nov '06

Hi, I am just wondering if there is any way that I can have two or more volume viewer windows open at the same time. I am comparing two density maps and to be able to change the threshold and color for both maps, without having to go back and forth in the same window, would be much easier and useful. Also, I recently fitted a pdb crystal structure into a density map but was not able to save it with relation to the density map (the feature which was available in previous releases). However, if I have multiple pdb files open then I can save the pdb file of my interest with respect to the map. Is there anyway to save a fitted pdb file with respect to a density map without opening other pdb files? Thank you, Batsal. -------------------------------------------------- Batsal Devkota Graduate Student, School of Biology GeorgiaInstitute ofTechnology Atlanta, GA 30332-0400

4 3

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

2 1

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 >> >> >

1 0

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

2 1

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

1 0

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

2 1

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

3 3

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"

2 1

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

2 4

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

2 2

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]; } } }

1 0

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.

1 1

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

3 4

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

3 2

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

2 1

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

2 1

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 ---------------------------

2 1

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 >

1 0

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 -------

2 1

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 -------

1 0

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 + 46 >32 libtcl8.4.dylib 0x0a0648a9 TclServiceIdle + 65 >33 libtcl8.4.dylib 0x0a055661 Tcl_DoOneEvent + 380 >34 libtk8.4.dylib 0x0b00ae3a Tk_UpdateObjCmd + 44 >35 libtcl8.4.dylib 0x0a00fa41 TclEvalObjvInternal + 769 >36 libtcl8.4.dylib 0x0a010694 Tcl_EvalObjv + 232 >37 _tkinter.so > 0x016f18ad Tkapp_Call + 199 (_tkinter.c: >1314) >38 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >39 python2.4 0x000638b1 PyEval_EvalFrame + 23100 >(ceval.c:3645) >40 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >41 python2.4 0x0006370c PyEval_EvalFrame + 22679 >(ceval.c:3656) >42 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >43 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >44 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >45 python2.4 0x000617c2 PyEval_EvalFrame + 14669 >(ceval.c:3840) >46 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >47 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >48 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >49 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >50 python2.4 0x000b89dc builtin_apply + 201 >(bltinmodule.c:100) >51 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >52 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >53 python2.4 0x000b6570 function_call + 320 >(funcobject.c:548) >54 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >55 python2.4 0x0000c662 instancemethod_call + 401 >(classobject.c:2447) >56 python2.4 0x00006549 PyObject_Call + 45 >(abstract.c:1795) >57 python2.4 > 0x0005d0ee PyEval_CallObjectWithKeywords >+ 112 (ceval.c:3430) >58 _tkinter.so 0x016efea4 PythonCmd + 220 (_tkinter.c: >2001) >59 libtcl8.4.dylib 0x0a00d10f TclInvokeStringCommand + 121 >60 libtcl8.4.dylib 0x0a00fa41 TclEvalObjvInternal + 769 >61 libtcl8.4.dylib 0x0a00fd57 Tcl_EvalEx + 503 >62 libtcl8.4.dylib 0x0a064f95 AfterProc + 106 >63 libtcl8.4.dylib 0x0a06477b TimerHandlerEventProc + 94 >64 libtcl8.4.dylib 0x0a055366 Tcl_ServiceEvent + 131 >65 libtcl8.4.dylib 0x0a05558f Tcl_DoOneEvent + 170 >66 _tkinter.so 0x016ef69f Tkapp_MainLoop + 188 >(_tkinter.c:2539) >67 python2.4 0x0006359e PyEval_EvalFrame + 22313 >(ceval.c:3563) >68 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >69 python2.4 0x0006370c PyEval_EvalFrame + 22679 >(ceval.c:3656) >70 python2.4 0x000638b1 PyEval_EvalFrame + 23100 >(ceval.c:3645) >71 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >72 python2.4 0x0006370c PyEval_EvalFrame + 22679 >(ceval.c:3656) >73 python2.4 0x000642ca PyEval_EvalCodeEx + 1774 >(ceval.c:2736) >74 python2.4 > 0x0006450a PyEval_EvalCode + 87 (ceval.c: >490) >75 python2.4 0x0008af5c PyRun_FileExFlags + 200 >(pythonrun.c:1265) >76 python2.4 > 0x0008b23f PyRun_SimpleFileExFlags + 640 >(pythonrun.c:860) >77 python2.4 0x00005974 Py_Main + 3199 (main.c:493) >78 python2.4 0x00001cc6 _start + 216 >79 python2.4 0x00001bed start + 41 > >Thread 1: >0 libSystem.B.dylib 0x90019d3c select + 12 >1 libSystem.B.dylib 0x90023d87 _pthread_body + 84 > >Thread 0 crashed with X86 Thread State (32-bit): > eax: 0x00000002 ebx: 0x940988bf ecx: 0x00000000 edx: 0x00000001 > edi: 0x00000000 esi: 0x608d1000 ebp: 0xbfffba68 esp: 0xbfffb720 > ss: 0x0000001f efl: 0x00010246 eip: 0x940a3fc4 cs: 0x00000017 > ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 > >Binary Images Description: > 0x1000 - 0xd2fff python2.4 /Applications/Chimera.app/Contents/ >Resources/bin/python2.4 > 0x392000 - 0x394fff libtr.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libtr.dylib > 0x3d8000 - 0x3dafff operator.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/operator.so > 0x3e4000 - 0x3e4fff _weakref.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_weakref.so > 0x3f0000 - 0x3f0fff _chimera.so /Applications/Chimera.app/Contents/ >Resources/lib/_chimera.so > 0x3f9000 - 0x3fbfff libwrappy2.dylib /Applications/Chimera.app/ >Contents/Resources/lib/libwrappy2.dylib > 0x505000 - 0x585fff libotf.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libotf.dylib > 0x5a8000 - 0x5b0fff libXext.6.dylib /usr/X11R6/lib/libXext.6.dylib > 0x5cd000 - 0x5ddfff libz.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libz.dylib > 0x5e5000 - 0x5e8fff strop.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/strop.so > 0x5f5000 - 0x5f6fff MacOS.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/MacOS.so > 0x705000 - 0x711fff libftgl.dylib /Applications/Chimera.app/Contents/ >Resources/lib/libftgl.dylib > 0x1008000 - 0x11b5fff _chimera.dylib /Applications/Chimera.app/ >Contents/Resources/lib/_chimera.dylib > 0x1300000 - 0x1340fff libfreetype.6.dylib > /Applications/Chimera.app/Contents/Resources/lib/libfreetype.6.dylib > 0x148b000 - 0x14e6fff libGLU.1.dylib /usr/X11R6/lib/libGLU.1.dylib > 0x1511000 - 0x156bfff libGL.1.dylib /usr/X11R6/lib/libGL.1.dylib > 0x159f000 - 0x165cfff libX11.6.dylib /usr/X11R6/lib/libX11.6.dylib > 0x1684000 - 0x16bcfff _vrml.so /Applications/Chimera.app/Contents/ >Resources/lib/_vrml.so > 0x16ec000 - 0x16f2fff _tkinter.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_tkinter.so > 0x1707000 - 0x1708fff math.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/math.so > 0x1710000 - 0x1711fff _random.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_random.so > 0x17f9000 - 0x17f9fff _imagingtk.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/PIL/_imagingtk.so > 0x2048000 - 0x204afff binascii.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/binascii.so > 0x2054000 - 0x2055fff fcntl.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/fcntl.so > 0x205d000 - 0x20a1fff _imaging.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/PIL/_imaging.so > 0x2133000 - 0x2136fff array.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/array.so > 0x2176000 - 0x2177fff _ssl.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_ssl.so > 0x220f000 - 0x2215fff _socket.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_socket.so > 0x222a000 - 0x222bfff time.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/time.so > 0x2275000 - 0x2276fff cStringIO.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/cStringIO.so > 0x2300000 - 0x232ffff libTix8.4.dylib /Applications/Chimera.app/ >Contents/Resources/lib/Tix8.4/libTix8.4.dylib > 0x250d000 - 0x2529fff GLDriver /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Resources/GLDriver.bundle/GLDriver > 0x2530000 - 0x2554fff GLRendererFloat /System/Library/Frameworks/ >OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat > 0x255b000 - 0x2561fff libTogl2.0.dylib /Applications/Chimera.app/ >Contents/Resources/lib/Togl2.0/libTogl2.0.dylib > 0x2568000 - 0x2576fff libXmu.6.dylib /usr/X11R6/lib/libXmu.6.dylib > 0x257e000 - 0x25b7fff libXt.6.dylib /usr/X11R6/lib/libXt.6.dylib > 0x25cb000 - 0x25cffff libSM.6.dylib /usr/X11R6/lib/libSM.6.dylib > 0x25d4000 - 0x25e3fff libICE.6.dylib /usr/X11R6/lib/libICE.6.dylib > 0x2705000 - 0x285efff GLEngine /System/Library/Frameworks/ >OpenGL.framework/Resources/GLEngine.bundle/GLEngine > 0x288a000 - 0x29fafff com.apple.GeForceFXGLDriver 1.4.40 (4.4.0) > /System/Library/Extensions/GeForceFXGLDriver.bundle/Contents/MacOS/ >GeForceFXGLDriver > 0x2b9b000 - 0x2b9cfff _collaboratory.so > /Applications/Chimera.app/Contents/Resources/lib/_collaboratory.so > 0x2c99000 - 0x2c9cfff _AE.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_AE.so > 0x2caf000 - 0x2cb0fff _Evt.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_Evt.so > 0x2cbe000 - 0x2cc0fff struct.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/struct.so > 0x2cd8000 - 0x2cdefff _File.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_File.so > 0x2e1f000 - 0x2e22fff _Res.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/lib-dynload/_Res.so > 0x33b2000 - 0x33b3fff collections.so /Applications/Chimera.app/ >Contents/Resources/lib/python2.4/lib-dynload/collections.so > 0x3505000 - 0x3509fff multiarray.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/multiarray.so > 0x3519000 - 0x3529fff _numpy.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/_numpy.so > 0x355e000 - 0x356afff umath.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/umath.so > 0x35d9000 - 0x3688fff lapack_lite.so /Applications/Chimera.app/ >Contents/Resources/lib/python2.4/site-packages/Numeric/lapack_lite.so > 0x3791000 - 0x3797fff ranlib.so /Applications/Chimera.app/Contents/ >Resources/lib/python2.4/site-packages/Numeric/ranlib.so > 0x37ee000 - 0x380efff _volume.so /Applications/Chimera.app/Contents/ >Resources/lib/_volume.so > 0x386e000 - 0x3891fff _surface.so /Applications/Chimera.app/Contents/ >Resources/lib/_surface.so > 0x3961000 - 0x3974fff _contour.so /Applications/Chimera.app/Contents/ >Resources/lib/_contour.so > 0xa000000 - 0xa081fff libtcl8.4.dylib /Applications/Chimera.app/ >Contents/Resources/lib/libtcl8.4.dylib > 0xb000000 - 0xb0a9fff libtk8.4.dylib /Applications/Chimera.app/ >Contents/Resources/lib/libtk8.4.dylib >0x8fe00000 - 0x8fe49fff dyld 46.9 /usr/lib/dyld >0x90000000 - 0x9016ffff libSystem.B.dylib > /usr/lib/libSystem.B.dylib >0x901bf000 - 0x901c1fff libmathCommon.A.dylib > /usr/lib/system/libmathCommon.A.dylib >0x901c3000 - 0x90200fff com.apple.CoreText 1.1.1 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/CoreText.framework/Versions/A/CoreText >0x90227000 - 0x902fcfff ATS /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/ >A/ATS >0x9031c000 - 0x90770fff com.apple.CoreGraphics 1.258.38 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics >0x90807000 - 0x908cffff com.apple.CoreFoundation 6.4.6 (368.27) > /System/Library/Frameworks/CoreFoundation.framework/Versions/A/ >CoreFoundation >0x9090d000 - 0x9090dfff com.apple.CoreServices 10.4 (???) > /System/Library/Frameworks/CoreServices.framework/Versions/A/ >CoreServices >0x9090f000 - 0x90a02fff libicucore.A.dylib > /usr/lib/libicucore.A.dylib >0x90a52000 - 0x90ad1fff libobjc.A.dylib /usr/lib/libobjc.A.dylib >0x90afa000 - 0x90b5efff libstdc++.6.dylib > /usr/lib/libstdc++.6.dylib >0x90bcd000 - 0x90bd4fff libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib >0x90bd9000 - 0x90c4cfff com.apple.framework.IOKit 1.4.6 (???) > /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit >0x90c61000 - 0x90c73fff libauto.dylib /usr/lib/libauto.dylib >0x90c79000 - 0x90f1ffff com.apple.CoreServices.CarbonCore 682.15 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >CarbonCore.framework/Versions/A/CarbonCore >0x90f62000 - 0x90fcafff com.apple.CoreServices.OSServices 4.1 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >OSServices.framework/Versions/A/OSServices >0x91003000 - 0x91041fff com.apple.CFNetwork 129.18 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >CFNetwork.framework/Versions/A/CFNetwork >0x91054000 - 0x91064fff com.apple.WebServices 1.1.3 (1.1.0) > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >WebServicesCore.framework/Versions/A/WebServicesCore >0x9106f000 - 0x910eefff com.apple.SearchKit 1.0.5 > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >SearchKit.framework/Versions/A/SearchKit >0x91128000 - 0x91146fff com.apple.Metadata 10.4.4 (121.36) > > /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/ >Metadata.framework/Versions/A/Metadata >0x91152000 - 0x91160fff libz.1.dylib /usr/lib/libz.1.dylib >0x91163000 - 0x91302fff com.apple.security 4.5.1 (29002) > /System/Library/Frameworks/Security.framework/Versions/A/Security >0x91400000 - 0x91408fff com.apple.DiskArbitration 2.1.1 > /System/Library/Frameworks/DiskArbitration.framework/Versions/A/ >DiskArbitration >0x9140f000 - 0x91435fff com.apple.SystemConfiguration 1.8.6 > /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/ >SystemConfiguration >0x91447000 - 0x9144efff libbsm.dylib /usr/lib/libbsm.dylib >0x91452000 - 0x914c8fff com.apple.audio.CoreAudio 3.0.4 > /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio >0x91519000 - 0x91519fff com.apple.ApplicationServices 10.4 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >ApplicationServices >0x9151b000 - 0x91547fff com.apple.AE 314 (313) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/AE.framework/Versions/A/AE >0x9155a000 - 0x9162efff com.apple.ColorSync 4.4.8 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/ColorSync.framework/Versions/A/ColorSync >0x91669000 - 0x916dcfff com.apple.print.framework.PrintCore 4.6 (177.13) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/PrintCore.framework/Versions/A/PrintCore >0x9170a000 - 0x917b3fff com.apple.QD 3.10.21 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/QD.framework/Versions/A/QD >0x917d9000 - 0x91824fff com.apple.HIServices 1.5.2 (???) > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/HIServices.framework/Versions/A/HIServices >0x91843000 - 0x91859fff com.apple.LangAnalysis 1.6.3 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis >0x91865000 - 0x91880fff com.apple.FindByContent 1.5 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/FindByContent.framework/Versions/A/FindByContent >0x9188b000 - 0x918c8fff com.apple.LaunchServices 181 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/LaunchServices.framework/Versions/A/LaunchServices >0x918dc000 - 0x918e8fff com.apple.speech.synthesis.framework 3.5 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis >0x918ef000 - 0x9192afff com.apple.ImageIO.framework 1.5.0 > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ >Frameworks/ImageIO.framework/Versions/A/ImageIO >0x9193c000 - 0x919eefff libcrypto.0.9.7.dylib > /usr/lib/libcrypto.0.9.7.dylib >0x91a34000 - 0x91a4afff libcups.2.dylib /usr/lib/libcups.2.dylib >0x91a4f000 - 0x91a6dfff libJPEG.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libJPEG.dylib >0x91a72000 - 0x91ad0fff libJP2.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libJP2.dylib >0x91ae2000 - 0x91ae6fff libGIF.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libGIF.dylib >0x91ae8000 - 0x91b65fff libRaw.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >Versions/A/Resources/libRaw.dylib >0x91b69000 - 0x91ba6fff libTIFF.dylib /System/Library/Frameworks/ >ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ >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/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libvMisc.dylib >0x91cca000 - 0x91ceefff libvDSP.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libvDSP.dylib >0x91cf6000 - 0x920fffff libBLAS.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libBLAS.dylib >0x92139000 - 0x924edfff libLAPACK.dylib /System/Library/Frameworks/ >Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/ >libLAPACK.dylib >0x9251a000 - 0x92597fff com.apple.DesktopServices 1.3.4 > /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/ >Versions/A/DesktopServicesPriv >0x925d8000 - 0x92808fff com.apple.Foundation 6.4.7 (567.28) > /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation >0x92914000 - 0x929f2fff libxml2.2.dylib /usr/lib/libxml2.2.dylib >0x92a0f000 - 0x92afcfff libiconv.2.dylib /usr/lib/libiconv.2.dylib >0x92b0c000 - 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/

2 1

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

2 1

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

2 1

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 ~~~~~~~~~~~~~~~~~~~~~~

2 1

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

2 2

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 --

2 4

Showing data set axes
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera supports a format for making geometric objects called BILD described in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Below is a 6 line BILD file that when opened in Chimera shows cylindrical arrows for the X (red), (green), and Z (blue) axes in the style of the program VMD. I made the axes 20 units long, with radius 1 and cone shaped tip with a radius of 2. Tom ----- File axes.bld: .color 1 0 0 .arrow 0 0 0 20 0 0 1 2 .color 0 1 0 .arrow 0 0 0 0 20 0 1 2 .color 0 0 1 .arrow 0 0 0 0 0 20 1 2 > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: Chimera length units > Date: Thu, 2 Nov 2006 17:30:29 -0800 > > i figured some of that but is good to hear it from the source. > > one last question - if i want to make an origin with axes (like a CAD > program might have) so i don't get lost after rotating my volumes a jillion > times and have to click 'orient', is there a way for me to make a > marker-based model (two markers for each axis) and put it slightly > off-origin (like in the -,-,- octant) so that i have a visual on my axes as > i rotate the scene? > > as in, is there a simple way for me to hand-write a marker model that i can > just load and fix to the scene? > > thanks, > > -jeff

1 0

X11 updated for Mac OS X, stereo now?
by David Belnap 02 Nov '06

02 Nov '06

Apple has released an update for X11 with the following comment: This update addresses several issues in the X11 for Mac OS X package, enabling it to better handle: - GLX stereo visuals - offscreen rendering to GLX Pbuffers and Pixmaps I downloaded it and tried to run Chimera (beta version 1 build 2199 2006/01/24) in stereo. It didn't work. Does the X11 update have the stereo-in-a-window capability now that Chimera needs? Is there a newer version of Chimera that will run in stereo on the Mac? David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David_Belnap(a)byu.edu ============================================

2 1

Re: [Chimera-users] Chimera length units
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera clipping and other tools use xyz coordinates and do not use voxel or pixel measures. The volume dialog region bounds panel and the volume dialog step size are exceptions where voxel index positions are used. The notion of a voxel is only relevant to density maps, not atomic models and clippping applies to all kinds of data, not just maps. Screen pixels are a 2 dimensional concept so it is an awkward measure to use especially with perspective 3-d viewing for measuring lengths. Tom > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: Chimera length units > Date: Thu, 2 Nov 2006 14:30:30 -0800 > > does this mean that I can't refer to a given coordinate by pixel/voxel > location without resetting the voxel size to '1 1 1' (which I might not want > to do - does chimera not keep the mrc file (or other voxel data) inside of a > similar kind of array) > > > -----Original Message----- > > From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] > > Sent: Thursday, November 02, 2006 1:46 PM > > Cc: chimera-users(a)cgl.ucsf.edu > > Subject: Chimera length units > > > > > > Hi Jeff, > > > > Chimera does not know what units you are using, the data > > coordinates are just numbers as far as it is concerned. If > > you open a PDB atomic model the coordinates are always > > Angstroms. If you open a density map, say an MRC file, the > > header may include the voxel size. That value could be in > > Angstroms or nanometers. Often maps don't have the true > > voxel size in the header, often they say it is 1. In such > > cases you can use the Chimera volume dialog menu entry > > "Features / Origin and Scale" to set the voxel size in > > Angstroms or nanometers so that the map can be aligned with > > other models or maps. If you open a PDB model in Angstroms > > and a map with the scale set in nanometers then the map will > > look 10 times smaller than it should be relative to the model. > > > > Tom

1 0

Chimera length units
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, Chimera does not know what units you are using, the data coordinates are just numbers as far as it is concerned. If you open a PDB atomic model the coordinates are always Angstroms. If you open a density map, say an MRC file, the header may include the voxel size. That value could be in Angstroms or nanometers. Often maps don't have the true voxel size in the header, often they say it is 1. In such cases you can use the Chimera volume dialog menu entry "Features / Origin and Scale" to set the voxel size in Angstroms or nanometers so that the map can be aligned with other models or maps. If you open a PDB model in Angstroms and a map with the scale set in nanometers then the map will look 10 times smaller than it should be relative to the model. Tom > From: Jeff > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Date: Thu, 2 Nov 2006 13:26:11 -0800 > > thanks Tom, > > sorry for a goofy question, but how do I know what units chimera is using > (for measuring distances, having the output is nice in Angstroms, but > sometimes (like with orienting a clipping plane) using unitless/pixels is > more handy for displacements/etc) > > thanks, > > -jeff

1 0

Per-model clipping plane command
by Thomas Goddard 02 Nov '06

02 Nov '06

Hi Jeff, There isn't yet a Chimera command for per-model clipping. Below is some Python code that can do it. Open a density map and then open this Python code in Chimera to clip it. Some more code can make it loop through different depths. There is some trickiness to making it update the graphics window in such a loop. Ask for details if you want that. Tom > From: Jeff > To: <goddard(a)cgl.ucsf.edu> > Subject: per-model clipping plane question (or similar) > Date: Thu, 2 Nov 2006 10:54:26 -0800 > > hi Tom, > > was wondering if I can control the per-model clipping plane > orientation/parameters/etc via command line or shortcuts - > > would like to be able to methodically push a clipping plane in 'slab mode' > through my model to compare it w/ other 2D/projection tools I use - I know I > can click 'orient' on the model and it will orient to a default > position/rotation (and I can click orient on the per-model clipping plane > and therefore register them both), but is there then a way that I can > specify (say, along one axis, like z) where the slab/clipping plane is > positioned, like in pixels? > > can I control the angular position of the clipping plane via command line, > too? > > thanks, > > Jeff ----- Python code clip.py. # ----------------------------------------------------------------------------- # Python function to control per-model clipping (like menu entry # Tools / Depiction / Per-Model Clipping). The clip plane rotates with # the model (PDB structure, density map, ...). # # Parameters: # model is a Chimera Model # origin is (x,y,z) of point on clip plane. # normal is (nx,ny,nz) pointing towards clipped (invisible) half of plane. # slab_thickness is in data length units (usually Angstroms). # # Origin and normal are relative to the data coordinate system, for example, # the x,y,z coordinates of a PDB atoms or axes of a density map. The clip # def set_clipping(model, origin, normal, slab_thickness = None): p = model.clipPlane from chimera import Point, Vector p.origin = Point(*origin) p.normal = Vector(*normal) model.clipPlane = p model.useClipPlane = True if slab_thickness == None: model.useClipThickness = False else: model.clipThickness = slab_thickness model.useClipThickness = True # ----------------------------------------------------------------------------- # Cap holes left when clipping a surface. Controls graphical interface # shown by menu entry Tools / Depiction / Surface Capping. # # Parameters: # cap_color is (r,g,b) or (r,g,b,a) where values in range 0-1 # cap_mesh is True or False for mesh or solid cap appearance # cap_subdivision of 2 makes cap mesh twice as fine for detailed coloring. # cap_offset in data length units (usually Angstroms) for large models # sometimes needs to be larger to avoid cap itself being clipped due to # finite floating point precision in OpenGL. # def show_surface_caps(show, cap_color = None, cap_mesh = False, cap_subdivision = 1, cap_offset = 0.001): from SurfaceCap.gui import capper_dialog d = capper_dialog(create = True) d.Close() use_color = (cap_color != None) if use_color: d.use_cap_color.set(use_color) d.cap_color.showColor(cap_color) if cap_mesh: d.cap_style.set('mesh') else: d.cap_style.set('solid') d.subdivision_factor.set(cap_subdivision) d.cap_offset.set(cap_offset) d.show_caps.set(show) # ----------------------------------------------------------------------------- # Example using set_clipping(). # from chimera import openModels mlist = openModels.list() m = mlist[0] set_clipping(m, (.5,0,1), (0,1,1), 8) show_surface_caps(True, (1,0,0), True) # Red mesh caps

1 0

Chimera under FreeBSD
by Devon Ryan 01 Nov '06

01 Nov '06

Has anyone had success getting chimera to run under FreeBSD? I can get the linux version to start (under the linuxulator), but it crashes after ~20 seconds when the bundled version of python core dumps. I'm running FreeBSD 6.1 on an intel architecture. Thanks -- Devon Ryan | dpryan(a)sg.uchicago.edu Neuro Grad Student, Ptacek Lab | dpryan(a)phy.ucsf.edu University of Chicago '02 | dpryan(a)alumni.uchicago.edu www.dpryan.com | dpryan(a)dpryan.com ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

3 2

question regarding chimera 1.2304-wim32.exe
by AJ Campbell 31 Oct '06

31 Oct '06

I have tried installing Chimera several times on my Windows machine but keep receiving an error message saying "Outline highlight not supported by hardware", any advice would be appreciated. ~ Arthur

3 3

atom name balloons
by Greg Pintilie 31 Oct '06

31 Oct '06

I was wondering why in the new release of Chimera ballons no longer pop up when the mouse is placed over an atom and is left there... is this an option that has to be set somewhere? I found it extremely usefull and now am missing it... Greg

2 1

problems with starting Chimera
by Mareike Goeritz 30 Oct '06

30 Oct '06

Hello, I'm interested in using Chimera, but after downloading and installing the software I'm unable to launch the program. I always get the following error message: "Microsoft Visual C++ Runtime Library: Assertion failed! Program: C:\Program Files\Chimera\bin\pythonw.exe File: togl.c Line: 2994 Expression: res==TRUE For information on how your program can cause an assertion failure, see the Visual C++ documentation on asserts (Press Retry to debug the application - JIT must be enabled)" I'm not familiar with C++, so I don't know what to do. Does anybody know what might be missing or what's the problem? Thank you for your help!! Mareike -- ******************************** Dr. Mareike Goeritz Department of Chemistry, MC 164-30 California Institute of Technology 1200 E. California Blvd. Pasadena, CA 91125 (626) 395-6032 Tel (626) 683-8753 Fax goeritz(a)caltech.edu ********************************

2 1

Chimera, 3dsmax, blender
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Lydia, It's been years since I've had access to a 3dsmax license, so I can't really make good comparisons between it and Blender. Fundamentally, they serve the same role, so I expect you would find using them similar, especially compared to PyMOL, Chimera, etc. Before getting into the benefits, you should be aware that compared to any software truly designed for chemical modeling, Blender has some serious drawbacks. There is no pre-existing set of structural tools that is standard for chemistry modeling software: if you want ribbons, you have to write a procedure that will generate them. I'm assuming you're already familiar with this, though, since you're using 3dsmax. As another sizeable negative, CSG in Blender is still somewhat flaky. I seem to remember having far fewer problems in 3d studio, even back around ~R5 or 6. On the benefit side, Blender's plugin/scripting system is extremely free of restrictions. The scripting system is pure Python, and many Python "plugins" are available. The true plugins are done in C, but are currently restricted to some post-processing features. You could also use the scripting system to access C libraries. These features really help to make up for the lack of built-in chemistry-centered tools. The other reason why you might prefer Blender over 3dsmax is that the scripting and plugin system is very much like Chimera, so if you're using both it's only one system to learn. Jonathan > Message: 8 > Date: Mon, 30 Oct 2006 14:47:06 -0800 > From: "Lydia Jablonski" <lydka(a)uoregon.edu> > Subject: [Chimera-users] Exporting VRML, Using Blender > > Jonathan and Greg- > > Thank you for your suggestions. I wanted to at least try them before I responded. > > Exporting VRML: I did try the export to VRML from version 1.2304 and it is good to know that it works for ribbons now. Unfortunately, the imported VRML meshes don't seem to respond to the mesh smoothing in 3ds max. With the .pdb --> .pov --> .3ds --> .max workflow I'm able to get a completely smooth surface on the ribbon. With the imported .wrl (VRML) I am able to see the triangulation on the surface, especially with shiny materials. Increasing the subdivision quality in Chimera makes these triangles smaller, but they are still visible. > > Blender: Can you explain more the advantages of Blender for rendering/animating molecular models? I've been using 3ds max for quite a while (since the DOS days) so I feel very comfortable with it. But the need to work with molecular models is new so I'm still bumping around trying to figure out what all the possibilities are. If another 3D animation program would work better with exported .pdb files I'd be willing to pick it up. > > Any more pointers would be much appreciated. > > -Lydia

1 0

Toolbar and Favorite on PC
by jean-francois menetret 30 Oct '06

30 Oct '06

Hello all, when running chimera on my PC (windows XP), my toolbar stopped being displayed. If I uninstall and reinstall chimera, my toolbar comes back until the next reboot. How can I fix that ? Is there to restore my preferences after launching chimera? Regards Jean-Francois Jean-Fran�ois M�n�tret, 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

2 4

Re: [Chimera-users] Chimera-users Digest, Vol 42, Issue 19
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Although this does not relate to your question on licensing, is there any particular reason you're using such a complicated workflow? Chimera can be used to generate basic geometry (sphere/cylinder) from PDB files via povray, but so could any import system you have for the 3D modeling software. You would also lose the benefit of chemistry-centered structure for manipulation or selection: chains, residues, etc. I've been using Blender to handle complicated chemical models for a while now, and it wasn't that difficult to implement the import of various data types. With BioPython pdb files become trivial, and volumetric data sets are (very) difficult but possible. Jonathan > Hello- > > Do any of you have an idea of how much a single commercial license for Chimera would cost? > > I'm a 3D artist/animator/biology student that works at in the art dept. of a biotech company. I'm interested in the exporting .pdb files to .pov, then converting to .3ds to import to 3ds max. > > Thanks, > > Lydia Jablonski

3 3

changing center of rotation
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Although I haven't used EMAnimator, you can set the center of rotation within Chimera using the Set Pivot action: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#actpivot There's also Tools/Movement/Rotation, and lastly, you can edit structures to insert artificial points at extreme high/low XYZ locations, which will in effect manually set the center used via the 'center of models' option. I wouldn't recommend the last option unless you have a good reason to do so, but it does work. Jonathan > Message: 1 > Date: Mon, 30 Oct 2006 11:52:42 -0800 (PST) > From: wendy ochoa <wencryo(a)yahoo.com> > Subject: [Chimera-users] rotating molecules for movies > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <20061030195242.57847.qmail(a)web37306.mail.mud.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view? > Thanks > > > >

1 0

Re: [Chimera-users] viewing grid density
by Thomas Goddard 30 Oct '06

30 Oct '06

Bala reports that the problem was in an Amber input file. > From: "bala" <bala(a)igib.res.in> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] viewing grid density > Date: Fri, 27 Oct 2006 19:59:38 +0530 > > Hello Thomas and Elaine, > > Thank you for your information. I rechecked the amber input files and i = > found a mistake there in rms fitting the coordinates in my trajectory. > > regards, > Bala

1 0

Re: [Chimera-users] rotating molecules for movies
by Thomas Goddard 30 Oct '06

30 Oct '06

Hi Wendy, Here are some Chimera commands that are useful for making movies with Movie Recorder: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/moviecomm… Here's a fancier Chimera movie script example. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/1gfl.com Here is the documentation for the Movie Recorder dialog and movie command: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html Tom

1 0

rotating molecules for movies
by wendy ochoa 30 Oct '06

30 Oct '06

Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view? Thanks

2 1