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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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saving 2 maps for difference
by Gabriel Lander 09 Jun '08

09 Jun '08

I have 2 density maps, and use the "fit in map" function to best align the 2 of them. I'd like to use this fitting to create a difference map, but the original maps are not the same size. Does anyone know how to save both maps to the same grid in Chimera? For now I've been using the "subregion selection" tool in combination with "resampling voxel size", but if someone has a more direct method it'd be much appreciated. Thanks, -gabe

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<< Plotting Gaussian MO >>
by Hatuey Hack 09 Jun '08

09 Jun '08

Hi all, I have a cube file with the Molecular Orbitals calculated with Gaussian. When I load the cub file into Chimera, I am only seen half of the orbital surface. I would like to know what should I do to get the whole molecular orbital surface colored (as usually) with only to colors (each on for one half). Regards, Hatuey

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gaussian orbitals, Chimera-users Digest, Vol 62, Issue 11
by Jonathan Hilmer 09 Jun '08

09 Jun '08

Hatuey, If I remember correctly, you need to open the density map twice, then contour at the same level for both maps: one at the positive value and the other negative. Each map is colored independently, so they can be depicted however you want. Jonathan On Mon, Jun 9, 2008 at 1:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > 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. << Plotting Gaussian MO >> (Hatuey Hack) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Jun 2008 10:24:29 -0300 > From: "Hatuey Hack" <hatuey.hack(a)gmail.com> > Subject: [Chimera-users] << Plotting Gaussian MO >> > To: chimera-users(a)cgl.ucsf.edu > Message-ID: > <612c95fa0806090624l5395ab11k6c9b235379e1a4fe(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > I have a cube file with the Molecular Orbitals calculated with Gaussian. > > When I load the cub file into Chimera, I am only seen half of the > orbital surface. > > I would like to know what should I do to get the whole molecular > orbital surface colored (as usually) with only to colors (each on for > one half). > > Regards, > > Hatuey > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 62, Issue 11 > ********************************************* >

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Molecular voodoo
by Tom Goddard 06 Jun '08

06 Jun '08

While debugging a bit of Chimera code I stumbled upon molecular voodoo. Stick pins in any evil molecule. Ask your doctor if this treatment may be right for you. A snake toxin (PDB 1a0m) has been fully cursed in the attached image. I attach the voodoo doll Chimera script for your amusement. You open voodoodoll.py in Chimera and then ctrl-right-mouse-button lets you place pins. Works in Chimera production release 1.2470 and newer. Tom def mouse_down_cb(viewer, event): from VolumeViewer import slice xyz_in, xyz_out = slice.clip_plane_points(event.x, event.y) from chimera import selection selection.clearCurrent() from VolumePath import place_marker place_marker(xyz_in) place_marker(xyz_out) from chimera import mousemodes as m m.addFunction('hide triangle', (mouse_down_cb, None, None)) m.setButtonFunction('3', ['Ctrl'], 'hide triangle')

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smoothening the edge of molecular surface
by Maurice Ho 06 Jun '08

06 Jun '08

Is there any way to smoothen the edge of molecular surface when only part of it would be displayed? It's quite often that a couple of triangles sticking out from the edges which makes the image a bit absurd. Please kindly advice. rgds, Maurice Ho

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