June 2008 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] how to draw lines in Chimera
by Elaine Meng 24 Jun '08

24 Jun '08

On Jun 24, 2008, at 4:24 PM, Qing Xie wrote: > Hi, > I'm trying to draw a bunch of axes from center (0,0,0). I could do > this > in 'O' by calling this macro: > > begin_object symax > colour blue > stick_xyz 139.05, -0.00, -16.25, -139.05, 0.00, 16.25, 0.25 > stick_xyz -111.40, 43.12, 73.02, 111.40, -43.12, -73.02, 0.25 > stick_xyz -107.48, 80.74, 39.10, 107.48, -80.74, -39.10, 0.25 > stick_xyz -66.72, 119.11, -31.00, 66.72, -119.11, 31.00, 0.25 > stick_xyz 50.41, 73.78, -107.77, -50.41, -73.78, 107.77, 0.25 > stick_xyz 100.65, 0.20, -97.31, -100.65, -0.20, 97.31, 0.25 > stick_xyz -68.88, 113.16, 45.26, 68.88, -113.16, -45.26, 0.25 > stick_xyz -39.02, 80.98, -107.34, 39.02, -80.98, 107.34, 0.25 > stick_xyz 10.15, 0.20, -139.64, -10.15, -0.20, 139.64, 0.25 > stick_xyz 50.47, -73.42, -108.00, -50.47, 73.42, 108.00, 0.25 > end_object symax > > Since I had to use some features in Chimera, do you know what > commands I > should combine to do similar things above? > Thank you! > Sincerely, > Qing Hi Qing, You can make a BILD file defining the objects, for example containing the following: .color medium blue .cylinder 139.05 -0.00 -16.25 -139.05 0.00 16.25 1 .cylinder -111.40 43.12 73.02 111.40 -43.12 -73.02 1 .cylinder -107.48 80.74 39.10 107.48 -80.74 -39.10 1 .cylinder -66.72 119.11 -31.00 66.72 -119.11 31.00 1 .cylinder 50.41 73.78 -107.77 -50.41 -73.78 107.77 1 .cylinder 100.65 0.20 -97.31 -100.65 -0.20 97.31 1 .cylinder -68.88 113.16 45.26 68.88 -113.16 -45.26 1 .cylinder -39.02 80.98 -107.34 39.02 -80.98 107.34 1 .cylinder 10.15 0.20 -139.64 -10.15 -0.20 139.64 1 .cylinder 50.47 -73.42 -108.00 -50.47 73.42 108.00 1 and open it in Chimera to create the objects. I also attached this below as the file sticks.bild to be opened directly in Chimera. I didn't think 0.25 looked that good, but you can edit the file to whatever radius (and color, etc.) that you want. The BILD language also includes many other objects: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html 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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Re: [Chimera-users] find levels and morph conformations
by Thomas Goddard 24 Jun '08

24 Jun '08

Hi Ed, The Morph Conformations tool works with submodels. It will not work between two models or submodels that have different numbers of chains. The error message you get means that you are giving it models with different numbers of chains. Tom Edward Brignole wrote: > Tom, > > ... I'd like to use morph conformations between two pdbs each > composed of the same submodels/chains. I've tried to do this through the > dialog but it displays an error telling me "cannot interpolate the > models have different numbers of chains". The only way I can see to do > this is to write the pdb as a mol2 so that all atoms are in a single > model without submodels, open the mol2, and run morph conformations. > Is there another method or is this the simplest? > > Thanks, > Ed

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selecting/displaying zones
by Elaine Meng 24 Jun '08

24 Jun '08

On Jun 24, 2008, at 11:56 AM, Thomas C. Marlovits wrote: > > Am using Chimera and would like to do the following: > - would first like to focus on specific side chain residues (for > example lysines) > - at a specific atom of either one or all lysines present in my > sample, I would like to draw a region of interest (which should be > a sphere with a given distance ... then make it rather transparent > like soap bobbles ...) ... the idea of this is to highlight areas > within a given distance away from this atom > - then I would like to read out all other side chains that are > within such an area ( in a table or so) ... and eventually > highlight them with specific colors ... > > Elaine, is there an easy way to do this ? > Tx, > -Thomas > ---------------------------------------------------------------------- > --------- > > Thomas C. Marlovits, PhD, M.A.S. > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences (IMBA) Hi Thomas, You can definitely (1) select the atoms or residues within a specified cutoff of some other atoms and write a list of what is selected to the Reply Log or to a file. Slightly trickier is (2) displaying a "bubble." (1) The following command selects all atoms within 4.5 angstroms of atom NZ in lysine 92, chain A (example structure 2gbp): select :92.a@nz za<4.5 to select the whole residues with any atom in the zone, use "z" or "zr" instead of "za", and to use all the atoms of that lysine, just omit "@nz" from the command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#zones This selection process can also be done by Ctrl-clicking to select the atom and then using Select... Zone. You can write out a list of the selection with Actions... Write List (click Log if you want to send it to the Reply Log instead). The default is a list of all the atoms individually, but you can set it to "residues" instead to just get one line of output per residue. The command to do that same thing is "writesel" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/writesel.html (2) The "bubble." I imagine something like Volume Eraser would be nice (check it out: Tools... Volume Data... Volume Eraser). However, that does not let you specify particular coordinates for the center. You have to move it around by hand. Volume Eraser really just makes a big atom and gives it a transparent color. You could add an atom in Build Structure (under Tools... Structure Editing), color it a transparent color, and change its radius with "vdwdefine" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ editing.html#build http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html It doesn't let you enter specific coordinates for the atom. However, if you add the atom as a "new model" you can match it to different locations on the first. For example, if the new atom is model 1 and the structure of interest (say 2gbp) is model 0: rep sphere #1 colordef tpink 1 .6 .6 .6 color tpink #1 vdwdef 3.0 #1 vdwdef +1 #1 vdwdef +1 #1 match #1 #0:147.a@nz select #1 za<5 & #0 [... etc. ...] The radius would just be for display purposes. You'd still have to specify the zone distance when selecting. A couple of failed ideas: (a) You can make a spherical surface of specified radius with the command "shape" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html but you cannot directly specify coordinates for the center or easily modify radius after it has been created. (b) Create a spherical object in BILD format. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Disadvantages are inability to make it transparent and having to delete/recreate the object just to change its radius. 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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how could u know the order of atoms?
by Kamal Al Nasr 23 Jun '08

23 Jun '08

Dear Sir/Madam, I am using Chimera viewer..and it is a great viewer ever... I kindly have a question... how could you know (from PDB file) the coorect bonding between atoms? I mean that how could you know that this atom is connected with CA not N nor C.....do u have all these bonds stored already in a database? or you use atom positions to determine that? I appreciate your time.... Kamal

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connectivity
by Jean Didier Pie Marechal 18 Jun '08

18 Jun '08

Dear all, I would like to use chimera to generate inputs for gaussian QM/MM calculations (ONIOM). One of the element I need is the connectivity of the atoms. I looked around the programmer's guide but couldn't find the right module that takes this in charge. what is the way to have access the connectivity of a given molecule? All the best, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Juny 18, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 18 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Find contour level to enclose a specified volume (Thomas > Goddard) 2. Re: Find contour level to enclose a specified volume > (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 17 Jun 2008 15:44:57 -0700 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: [Chimera-users] Find contour level to enclose a specified > volume > To: "'Chimera BB'" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <48583E69.5090608(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Ed Brignole asked about setting a volume contouring level so that > the > resulting surface encloses a desired volume (cubic Angstroms). > Attached > is a Python script that does this in two ways. The first way is > fast > but approximate finding the level such that the number of enclosed > grid > points times the voxel volume equals the requested volume. > Estimating > the enclosed volume of the surface this way can give a much > different > result than actually computing analytically the volume within the > surface. The second approach computes surfaces at different > contour > levels and calculates analytically the volume. It uses bisection > to > find the correct contour level. This approach can be slow, about > 30 > seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface > triangles. Most of that time (80%) is actually computing the > enclosed > volume. That should be very fast but the code is checking for > holes in > the surface in a rather slow way. Both methods use the step size > (subsampling) set in the volume dialog. > > Tom >

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Find contour level to enclose a specified volume
by Thomas Goddard 18 Jun '08

18 Jun '08

Ed Brignole asked about setting a volume contouring level so that the resulting surface encloses a desired volume (cubic Angstroms). Attached is a Python script that does this in two ways. The first way is fast but approximate finding the level such that the number of enclosed grid points times the voxel volume equals the requested volume. Estimating the enclosed volume of the surface this way can give a much different result than actually computing analytically the volume within the surface. The second approach computes surfaces at different contour levels and calculates analytically the volume. It uses bisection to find the correct contour level. This approach can be slow, about 30 seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface triangles. Most of that time (80%) is actually computing the enclosed volume. That should be very fast but the code is checking for holes in the surface in a rather slow way. Both methods use the step size (subsampling) set in the volume dialog. Tom # ----------------------------------------------------------------------------- # Find threshold level so that a contour surface encloses a specified volume. # # Method: Estimates how many grid points should lie within # surface then finds the level having that many grid points with higher values. # This method can produce a level where the enclosed volume is very # different from the requested volume. # def level_enclosing_grid_points(v, vol): (x0,y0,z0), (x1,y1,z1) = v.xyz_bounds() tvol = (x1-x0)*(y1-y0)*(z1-z0) r = 1.0 - vol/tvol s = v.matrix_value_statistics() level = s.rank_data_value(r) return level # ----------------------------------------------------------------------------- # Find threshold level so that a contour surface encloses a specified volume. # # Method: Computes surfaces for different levels and resulting volumes # using bisection to determine the correct level. # def level_by_bisection(v, vol, iterations = 10): m = v.matrix() l0, l1 = m.min(), m.max() ijk_step = v.region[2] from numpy import product voxel_volume = product(ijk_step) * product(v.data.step) mvol = vol / voxel_volume return find_level(m, l0, l1, mvol, iterations) # ----------------------------------------------------------------------------- # def find_level(m, l0, l1, mvol, iterations): l = 0.5*(l0+l1) if iterations <= 1: return l from _contour import surface varray, tarray = surface(m, l, cap_faces = True) from _surface import enclosed_volume vl, hole_count = enclosed_volume(varray, tarray) varray = tarray = None if vl == mvol: return l if vl > mvol: l0 = l else: l1 = l return find_level(m, l0, l1, mvol, iterations - 1) # ----------------------------------------------------------------------------- # vol = 3.227e6 # sfv.mrc, threshold level 1000. from chimera import openModels from VolumeViewer import volume_list for v in volume_list(): level1 = level_enclosing_grid_points(v, vol) level2 = level_by_bisection(v, vol) print v.name, level1, level2

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3D surfaces from MacMolPlt or Gamess
by David Chenoweth 13 Jun '08

13 Jun '08

Dear Chimera team, I am having a bit of trouble reading a file into Chimera. Currently I am using Gamess to run DFT calculations and I can open these files in MacMolPlt which allows me to display orbitals or plot electrostatic potential surfaces. I can export the 3D surface data however I can't get Chimera to read the 3D grid files. Can you help me? I attached the file format info below and I can send you example files if you need. I am really trying to use Chimera for all my graphics needs wether it be viewing surfaces or orbitals from DFT calculations or looking at electron density maps from crystal structure data. If I could convert the 3D surface data files below into ccp4 or cns formated files that should also work for Chimera I just haven't found a way to do this yet. Thanks in advance, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu ********************************************** File format data info: http://www.scl.ameslab.gov/~brett/MacMolPlt 2D and 3D Surfaces (Import and Export) MacMolPlt implements a simple format for importing and exporting 2D and 3D surface data. To export a surface first create a surface and make sure that the surface is updated so that the grid data is available for export. Then choose the Export menu command and the Surface export format. MacMolPlt will then export the surface grid data to the file you specify (this is useful to check the input format as well). To import a 2D or 3D surface create a new General 2D or 3D surface. From the surface dialog you can then choose the file containing the grid data. The format for the 2D and 3D files are similar but there are a couple of differences. Floating point numbers may be given in a variety of formats and the grid data may contain any number of values per line. The units for the coordinate system should normally be angstroms. For 2D planes the format is: 1Line Label 30 # grid points -4.165882 -4.306789 0.839681 //Origin of the 2D grid 0.297019 0.000000 0.000000 //X inc vector 0.000000 0.297019 0.000000 //Y inc vector -0.000018 -0.000021... (# of grid points squared grid values) For 3D surfaces: 1 Line label 35 12 41 //nx ny nz -4.687880 -1.587537 -5.059790 //Origin of the 3D grid 0.280144 0.288642 0.275207 //x increment, y inc, z inc/ grid(x(y(z))) 0.000000 0.000000... (nx*ny*nz grid values)

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3D surfaces from MacMolPlt or Gamess
by David Chenoweth 12 Jun '08

12 Jun '08

Dear Chimera team, I am having a bit of trouble reading a file into Chimera. Currently I am using Gamess to run DFT calculations and I can open these files in MacMolPlt which allows me to display orbitals or plot electrostatic potential surfaces. I can export the 3D surface data however I can't get Chimera to read the 3D grid files. Can you help me? I attached the file format info below with an exported density file and electrostatic potential map. I am really trying to use Chimera for all my graphics needs wether it be viewing surfaces or orbitals from DFT calculations or looking at electron density maps from crystal structure data. If I could convert the 3D surface data files below into ccp4 or cns formated files that should also work for Chimera I just haven't found a way to do this yet. Thanks in advance, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu ********************************************** File format data info: http://www.scl.ameslab.gov/~brett/MacMolPlt 2D and 3D Surfaces (Import and Export) MacMolPlt implements a simple format for importing and exporting 2D and 3D surface data. To export a surface first create a surface and make sure that the surface is updated so that the grid data is available for export. Then choose the Export menu command and the Surface export format. MacMolPlt will then export the surface grid data to the file you specify (this is useful to check the input format as well). To import a 2D or 3D surface create a new General 2D or 3D surface. From the surface dialog you can then choose the file containing the grid data. The format for the 2D and 3D files are similar but there are a couple of differences. Floating point numbers may be given in a variety of formats and the grid data may contain any number of values per line. The units for the coordinate system should normally be angstroms. For 2D planes the format is: 1Line Label 30 # grid points -4.165882 -4.306789 0.839681 //Origin of the 2D grid 0.297019 0.000000 0.000000 //X inc vector 0.000000 0.297019 0.000000 //Y inc vector -0.000018 -0.000021... (# of grid points squared grid values) For 3D surfaces: 1 Line label 35 12 41 //nx ny nz -4.687880 -1.587537 -5.059790 //Origin of the 3D grid 0.280144 0.288642 0.275207 //x increment, y inc, z inc/ grid(x(y(z))) 0.000000 0.000000... (nx*ny*nz grid values)

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Swapaa from Java Runtime.exec
by ProtEUS 11 Jun '08

11 Jun '08

Hello all! I am sorry if this is a dump question, but is it possible for swapaa to run fromJava server with Runtime.exec()? Thank you very much!! Andreas, Greece.

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translation + rotation of a whole scene
by Nils Becker 11 Jun '08

11 Jun '08

Hi list, I have a question about rotating and translating a bunch of models together while preserving their spatial relations. In particular, I would like to apply a matrix almost as in the matrixset command. THe difference is that I do not want to apply it individually to each model, but to one chosen models, while having the rest move together with the chosen model. Is that feasible in chimera? cheers, Nils

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Chimera-users June 2008