May 2007 - Chimera-users - RBVI Mailing Lists

new feature: conversion of atomic coordinates to electron density map
by Thomas C Marlovits 13 Jun '07

13 Jun '07

Hi, I am not quite sure, whether this is possible with Chimera ... but it would be great if there is a feature that would allow to convert a .pdb structure (atomic coordinates) into a map usually obtained by electron microscopy (sections) - for example into mrc/ccp4 format. Even filtering this map then to different resolutions (including storing entire maps) would be an interesting feature. Thanks, -Thomas __________________________________________ Thomas C Marlovits, PhD, M.A.S IMP - Institute of Molecular Pathology IMBA - Institute of Molecular Biotechnology, Austrian Academy of Sciences Dr. Bohr-Gasse 3 A-1030 Vienna AUSTRIA marlovits(a)imp.univie.ac.at Tel (+ 43) 1 79044 4630

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ESP grid is offset from original PDB coordinates??
by Kenward Vaughan 30 May '07

30 May '07

I was playing with esp results yesterday from Delphi on several structures, and ran a quick calculation on 2ace. To my surprise, the results as visualized as a solid under volume viewer were very obviously offset from the structure itself. They stand alone to one side of the original. I've attached a small jpg of this. I'm using the latest Linux production version (beta version 1 build 2415) on an amd64 box (Debian Sid, kernel 2.6.20). I hope there is a simple explanation... ;-) I am no expert with Delphi, so something may be odd there. I used a couple of the siz/crg files, with the same results in each case, so I suspect something in the original pdb file is messing things up? Cheers! Kenward -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$???

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Python script for reading volume values at atom positions
by Tom Goddard 30 May '07

30 May '07

Hi Terry, Here is a Python script to read a volume map and a PDB file and print the values of the map interpolated at the atom positions. It will work without the Chimera graphical user interface. I tested it in Chimera 1.2415. Tom # ----------------------------------------------------------------------------- # Script that opens PDB and map files and prints the map values interpolated # at each atom position. Can be run without graphical user interface: # # chimera --nogui avalnogui.py # def map_values_at_atoms(pdb_path, map_path): # Open map file. # File name has to have file suffix indicating volume format. from VolumeData import open_file data = open_file(map_path) from VolumeViewer import Data_Region, full_region, Rendering_Options ro = Rendering_Options() map = Data_Region(data, full_region(data.size), '', ro) attribute_name = data.name.split('.')[0] # Open PDB model(s). from chimera import openModels molecules = openModels.open(pdb_path, 'PDB') # Interpolate map values at atom positions. from AtomDensity import set_atom_volume_values for mol in molecules: set_atom_volume_values(mol, map, attribute_name) # Print values. for mol in molecules: for a in mol.atoms: v = getattr(a, attribute_name) print '%-15s %12.4g' % (a.oslIdent(), v) # ----------------------------------------------------------------------------- # map_path = '/usr/local/src/chimera-demos/volume/examples/1a0m.omap' pdb_path = '/usr/local/src/chimera-demos/volume/examples/1a0m.pdb' map_values_at_atoms(pdb_path, map_path)

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Color in Chimera
by Albion Baucom 25 May '07

25 May '07

How do I determine the exact color value of a model from a previous session? I want to open a session, determine the color of a selected chain, and then color another chain that exact color. I can't seem to find an "eye-dropper" or other comparable tool to determine the color value (RGB, hex, etc). Thanks. Albion

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Chimera release candidate
by Elaine Meng 24 May '07

24 May '07

Hello everybody, A new version of Chimera (1.2415) is available for all platforms: http://www.cgl.ucsf.edu/chimera/download.html It is a candidate for a production release we plan to make in about a week. Many new features have been added since our last production release (1.2304, October 2006), as detailed in the release notes: http://www.cgl.ucsf.edu/chimera/1.2415/docs/relnotes/snapshot.html Here are just a few of the changes since last October: - embedded POV-Ray for production of glossy, shadowed images including labels - ability to supersample or to use POV-Ray when recording movies - new input formats: MDL MOL/SDF, Gromacs trajectories - new Fetch by ID types: EDS (fo-fc) electron density difference map, PQS predicted biological unit - Presets menu with display settings for interactive Chimera use or generation of publication images - Side View includes "top view" for interactively adjusting stereo parameters and perspective - expanded morphing capabilities - new Fit Map in Map tool - new windowsize command - updates to handle new naming conventions in the remediated PDB Enjoy! (and do let us know right away via "Report a Bug" or chimera- bugs(a)cgl.ucsf.edu if you find any problems) Thanks, 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] fit map in map
by Thomas Goddard 24 May '07

24 May '07

Hi Gabor, There are no Chimera commands to fit one map into another, but it can be done with a Python script. I've attached a Python script that I made by piecing together code from gui.py and __init__.py from directory chimera/share/FitMap. Tom Gabor Papai wrote: > Hi Tom, > > Can the fit map in map tool be used without the GUI and retreive back > only the transformation matrix? > Bye, > Gabor > # ----------------------------------------------------------------------------- # Example script for fitting one map in another without the graphical user # interface. # # chimera --nogui fitnogui.py # # It can also be run using the graphical Chimera interface using File/Open. # def fit_map_in_map(map1_path, map2_path, initial_map1_transform = None, map1_threshold = None, ijk_step_size_min = 0.01, # Grid index units ijk_step_size_max = 0.5, # Grid index units max_steps = 100, optimize_translation = True, optimize_rotation = True): # Files have to have file suffix indicating volume format. from VolumeData import open_file data1 = open_file(map1_path) data2 = open_file(map2_path) from VolumeViewer import Data_Region, full_region, Rendering_Options ro = Rendering_Options() map1 = Data_Region(data1, full_region(data1.size), '', ro) map2 = Data_Region(data2, full_region(data2.size), '', ro) if initial_map1_transform: from PDBmatrices.matrices import chimera_xform xf = chimera_xform(initial_map1_transform) map1.surface_model().openState.globalXform(xf) use_threshold = (map1_threshold != None) from FitMap import map_points_and_weights, motion_to_maximum points, point_weights = map_points_and_weights(map1, use_threshold) if len(points) == 0: if use_threshold: print 'No grid points above map threshold.' else: print 'Map has no non-zero values.' return move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps, ijk_step_size_min, ijk_step_size_max, optimize_translation, optimize_rotation) if initial_map1_transform: from PDBmatrices.matrices import multiply_matrices move_tf = multiply_matrices(move_tf, initial_map1_transform) header = ('\nFit map %s in map %s using %d points\n' % (map1.full_name(), map2.full_name(), stats['points']) + ' correlation = %.4g, overlap = %.4g\n' % (stats['correlation'], stats['overlap']) + ' steps = %d, shift = %.3g, angle = %.3g degrees\n' % (stats['steps'], stats['shift'], stats['angle'])) print header from FitMap.gui import transformation_description tfs = transformation_description(move_tf) print tfs # ----------------------------------------------------------------------------- # Example call fitting map into itself. # p1 = p2 = '/usr/local/src/chimera-demos/volume/examples/groel.mrc' fit_map_in_map(p1, p2)

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Electrostatical surface of a virus
by Eduardo Sanz-Garcia 23 May '07

23 May '07

I need to visualize the electrostatic surface of a virus. I don't know how to do it. I was thinking in the following sequence of instructions: 1. Use the DelPhiController to generate the potential map (*.phi) for the asymmetric unit. 2. Use Multiscale Models tool to generate the 60-related units. Is this a logic sequence ? Any hint would be appreciated. Thank you.

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Mac stereo
by Greg Couch 23 May '07

23 May '07

To deal with the issue that the Mac OS X's X11 doesn't work with stereo very well, we have decided to release an Aqua version of chimera concurrent with production releases of the X11 version. The Aqua version will be labeled as a snapshot because we still recommend using the X11 version (the user interface works much better than the Aqua version). But if you need stereo, multisampling (full window antialiasing), or background transparency/opacity, then you need to use the Aqua version. Greg Couch UCSF Computer Graphics Lab

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Re: [Chimera-users] Virus Images for the MSD Database
by Tom Goddard 23 May '07

23 May '07

Hi Jawahar, Unfortunately Chimera is not able to save images without displaying the graphical user interface. The image saving code grabs the image directly from the main window OpenGL graphics buffer, so it also will not work if the main window is covered or iconified. Greg Couch once made a special version of Chimera for Linux using the OSMesa graphics library that could do all the graphics off-screen including saving images. But I don't see that version in the Chimera download archive, and I believe it was made more than a year ago. We recently added raytraced image capture using POVray. Since that does not use the OpenGL graphics it should be able to work in nogui mode but a Chimera bug report indicates that does not work http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=3678&database=chime… and is expected to be difficult to fix. Unfortunately the only option at this time is to have the Chimera window appear to save an image. Tom Jawahar Swaminathan wrote: > Dear Tom, > We are interested in making virus capsid pictures for the MSD Database > atlas pages using chimera. For this purpose, I was recently provided > with a script from Cathy Lawson (RCSB) which makes really pretty > images of viral capsids. I attach the script given by Cathy below. > > However, since we would want to run chimera in an automatic manner > (ideally with the --nogui) option, I've been trying to run the script > with --nogui and this appears to conflict with the module tkgui which > is called in the program. > > So my question: is it possible to make images without necessarily > opening up a GUI ? > > I would be really grateful if you could clear this us.. > > best regards, > > Jawahar Swaminathan > PDB Depositions > Macromolecular Structure Database > EBI

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Problem with DCD not containing periodic box info when I use MD
by Antoine Daina 22 May '07

22 May '07

Hi Eric, I got a "DCD format error 9" returned by MD Movie in Chimera 1.2304 when trying to see the trajectory of a Charmm simulation without periodic box info. Can we easily fix it ? Antoine Daina, PhD, University of Geneva.

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Chimera-users May 2007