December 2008 - Chimera-dev - RBVI Mailing Lists

add h
by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

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examples of 2-D plotting in plugins?
by Randy Heiland 14 Jan '09

14 Jan '09

Hi gang, For one of the Chimera plugins that I now maintain, I'm considering eliminating the use of matplotlib and wondering if Chimera's innards are capable of doing what I want. For starters, are there any example plugins, etc that demonstrate how one could do simple plotting and simple (image) contours? In addition, I'd need to handle mouse events, e.g. to retrieve x,y positions on the contour image. thanks, Randy

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Buildstructure and xform coordinates
by Dr. Jean-Didier Maréchal 09 Jan '09

09 Jan '09

Dear all, Based on early queries, I am now using xform coord for most of my scripts. However, now I have a problem because I have mixture between xforms and coord. For example, I want to place a helium at the center of mass of the molecular and having previously calculated it using xform coordinates... The center of mass is therefore located at another part of the space. How could I transform on set of coords to the other? Thanks for any help! JD Here is the script from chimera import selection from chimera import Point, Vector, Xform import BuildStructure def com(sub): for i in range(len(sub.atoms)): sumi=0 center = Vector(0, 0, 0) for a in sub.atoms: sumi += a.element.mass center += a.element.mass * Vector(*a.xformCoord().data()) center_point=Point(center[0]/sumi,center[1]/sumi,center[2]/sumi) return center_point def placing_points(center): #pt=Point(center[0]/sum,center[1]/sum,center[2]/sum) #print pt BuildStructure.placeHelium('com', model='scratch', position=center) ligand = selection.currentResidues()[0] center=com(ligand) placing_points(center)

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Re: [chimera-dev] voodoo? Found workaround
by Thomas Goddard 15 Dec '08

15 Dec '08

Hi Miguel, Glad you found bild -- it can make nice arrowheads which the volume tracer approach you tried first (voodoo) can't do that. Bild graphics are rendered with VRML and that is immutable in Chimera -- you can not change shape or colors or move VRML/BILD objects. You can move the arrows as you found by putting each in its own model and using the "active" buttons in model panel. There aren't good solutions to these problems. You could go back to the volume tracer approach and get movable, stretchable, recolorable rods but without arrowheads. In the future we wish to make BILD objects independently movable, deletable, colorable, and possibly resizable. I suspect this is at least a year away. By the way, you can avoid using a temporary file with BILD by using a StringIO object. Here's an example: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002447.html Tom Miguel Ortiz Lombardia wrote: > Dear Tom, > > Don't bother, I found how to do that with bild objects: > > 8<----------------------------- > def needle(center,item): > > f = open( "/tmp/tmp" + str(item) + ".bild", 'w' ) > f.write( ".color green\n" ) > f.write( ".sphere %6.2f %6.2f %6.2f 1\n" % > (center[0]+15,center[1]+15,center[2]+15) ); > f.write( ".arrow %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f .5 1.5 0.6\n" > % ( center[0]+15,center[1]+15,center[2]+15, > center[0],center[1],center[2]) ) > f.close() > > from chimera import selection, UserError > from Midas.midas_text import makeCommand > > atoms = [a for a in selection.currentAtoms()] > if not atoms: > raise UserError("No atoms selected") > > item = 0 > for a in atoms: > item += 1 > needle(a.coord(),item) > makeCommand( 'open /tmp/tmp' + str(item) + '.bild' ) > ----------------------------->8 > > However, it would be nice, for this purpose, that bild objects were > 'stretchable' and that they would have a defined center of rotation, so > they can be moved around. For the second thing, I can simply select the > corf manually for each arrow, which is suboptimal, but not bad if you > don't have many 'needles'. For the first problem, 'stretchability' I > have to re-write the script for every particular 'needle' or rather > > ------------------------------------------------------------------------ > > find a compromise length... > Perhaps there is a more elegant way of doing all these manipulations > already implemented in chimera? > > I'm attaching a figure to show what I am looking for :-) > > Best regards, > > > > Miguel > > > > Début du message réexpédié : > >> De : Miguel Ortiz Lombardia <miguel.ortiz-lombardia(a)afmb.univ-mrs.fr> >> Date : 14 décembre 2008 15:09:20 HNEC >> À : Thomas Goddard <goddard(a)cgl.ucsf.edu> >> Objet : voodoo? >> >> Dear Tom, >> >> I'm naively trying to modify your molecular voodoo script to have >> needles pointing to selected residues (specifically to their CA atoms) >> I would really appreciate if you can help me with two probably simple >> questions. Firstly, this is my current code >> >> 8<----------------------------- >> def needle(center): >> >> xyz_in = center >> xyz_out = center[0]+5,center[1]+5,center[2]+5 >> >> from chimera import selection >> selection.clearCurrent() >> from VolumePath import place_marker >> place_marker(xyz_in) >> place_marker(xyz_out) >> >> from chimera import selection, UserError >> atoms = [a for a in selection.currentAtoms() if a.name == 'CA'] >> if not atoms: >> raise UserError("No CA atoms selected") >> >> for a in atoms: >> needle(a.coord()) >> ------------------------------>8 >> >> And these are the questions: >> >> 1. Why the positions of the m1 markers don't correspond to those of >> the CA atoms? >> 2. How could I modify the code to make every marker go to a different >> set, so I can then rotate them one by one appropriately so the figure >> shows the 'needles' in different directions, so that I can label them >> later on without overlap? >> >> I hope it isn't too silly... >> >> Cheers, >> >> >> -- >> Miguel Ortiz Lombardía >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> !!! NEW ADDRESS !!! >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> Architecture et Fonction des Macromolécules Biologiques >> UMR6098, CNRS, Université Aix-Marseille I & II >> Case 932 >> 163 Avenue de Luminy >> 13288 Marseille cedex 9 >> France >> Tel : +33(0) 491 82 55 93 >> Fax: +33(0) 491 26 67 20 >> e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr >> Web: http://www.pangea.org/mol/spip.php?rubrique2 >> > > -- > Miguel Ortiz Lombardía > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!! NEW ADDRESS !!! > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > Architecture et Fonction des Macromolécules Biologiques > UMR6098, CNRS, Université Aix-Marseille I & II > Case 932 > 163 Avenue de Luminy > 13288 Marseille cedex 9 > France > Tel : +33(0) 491 82 55 93 > Fax: +33(0) 491 26 67 20 > e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr > Web: http://www.pangea.org/mol/spip.php?rubrique2 >

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Drawing arrows to point at atoms
by Thomas Goddard 15 Dec '08

15 Dec '08

Hi Miguel, The trouble with your code was you needed to use needle(a.xformCoord()) instead of needle(a.coord()) The a.coord() gives the coordinates in the molecule's local coordinates while a.xformCoord() gives the coordinates in global Chimera coordinates which is what the place_marker() routine wants. Tom Miguel Ortiz Lombardia wrote: > Dear Tom, > > I'm naively trying to modify your molecular voodoo script to have > needles pointing to selected residues (specifically to their CA atoms) I > would really appreciate if you can help me with two probably simple > questions. Firstly, this is my current code > > 8<----------------------------- > def needle(center): > > xyz_in = center > xyz_out = center[0]+5,center[1]+5,center[2]+5 > > from chimera import selection > selection.clearCurrent() > from VolumePath import place_marker > place_marker(xyz_in) > place_marker(xyz_out) > > from chimera import selection, UserError > atoms = [a for a in selection.currentAtoms() if a.name == 'CA'] > if not atoms: > raise UserError("No CA atoms selected") > > for a in atoms: > needle(a.coord()) > ------------------------------>8 > > And these are the questions: > > 1. Why the positions of the m1 markers don't correspond to those of the > CA atoms? > 2. How could I modify the code to make every marker go to a different > set, so I can then rotate them one by one appropriately so the figure > shows the 'needles' in different directions, so that I can label them > later on without overlap? > > I hope it isn't too silly... > > Cheers, > > > -- > Miguel Ortiz Lombardía > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!! NEW ADDRESS !!! > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > Architecture et Fonction des Macromolécules Biologiques > UMR6098, CNRS, Université Aix-Marseille I & II > Case 932 > 163 Avenue de Luminy > 13288 Marseille cedex 9 > France > Tel : +33(0) 491 82 55 93 > Fax: +33(0) 491 26 67 20 > e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr > Web: http://www.pangea.org/mol/spip.php?rubrique2 > >

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Re: [chimera-dev] [Chimera-users] drawing a symmetry axis
by Mark Moll 13 Dec '08

13 Dec '08

Tom (and other Chimera developers), You might be interested in the paper below. It describes a method for computing the best axis of symmetry and computing a `symmetrized' version of a symmetric complex (i.e. with deviations from symmetry removed). They have extended the analysis since this paper appeared to other forms of symmetry, but this hasn't appeared yet, AFAIK. (The authors are cc-ed in case they want to follow up.) The first author may have a reference matlab implementation that could probably without too much trouble be converted into python using numpy. @article{shah2006a-symmetry-preserving-singular-value, Abstract = {A reduced order representation of a large data set is often realized through a principal component analysis based upon a singular value decomposition (SVD) of the data. The left singular vectors of a truncated SVD provide the reduced basis. In several applications such as facial analysis and protein dynamics, structural symmetry is inherent in the data. Typically, reflective or rotational symmetry is expected to be present in these applications. In protein dynamics, determining this symmetry allows one to provide SVD major modes of motion that best describe the symmetric movements of the protein. In face detection, symmetry in the SVD allows for more efficient compression algorithms. Here we present a method to compute the plane of reflective symmetry or the axis of rotational symmetry of a large set of points. Moreover, we develop a symmetry preserving singular value decomposition (SPSVD) that best approximates the given set while respecting the symmetry. Interesting subproblems arise in the presence of noisy data or in situations where most, but not all, of the structure is symmetric. An important part of the determination of the axis of rotational symmetry or the plane of reflective symmetry is an iterative reweighting scheme. This scheme is rapidly convergent in practice and seems to be very effective in ignoring outliers (points that do not respect the symmetry). }, Author = {Mili I. Shah and Danny C. Sorensen}, Doi = {10.1137/050646676}, Journal = {{SIAM} Journal on Matrix Analysis and Applications}, Number = {3}, Pages = {749--769}, Title = {A Symmetry Preserving Singular Value Decomposition}, Url = {http://link.aip.org/link/?SML/28/749/1}, Volume = {28}, Year = {2006} } On Dec 11, 2008, at 6:49 PM, Thomas Goddard wrote: > Hi Philip, > > I don't know an easy way to show the symmetry axis of your dimer > as a > line or rod using the normal Chimera commands. But you could do > this by > modifying the keyboard shortcut ai Python code. > > You would edit the file > > chimera/share/MatchDomains/__init__.py > > or on the Mac it would be > > Chimera.app/Contents/Resources/share/MatchDomains/__init__.py > > (and on the Mac you'd need to click the Chimera icon and choose "Show > package contents" to see in the Chimera.app folder). > > You would change the transform_schematic() routine (line 171) code > from > > # tarray = ((0,1,2),(0,2,3)) > tarray = ((0,1,2),(0,2,3),(0,1,5),(0,5,4),(1,2,6),(1,6,5), > (2,3,7),(2,7,6),(3,0,4),(3,4,7),(4,5,6),(4,6,7)) > g1 = sm.addPiece(varray, tarray, from_rgba) > # g1.displayStyle = g1.Mesh > > from Matrix import xform_matrix, apply_matrix > tf = xform_matrix(xform) > corners2 = [apply_matrix(tf, p) for p in corners] > varray2 = corners2 > g2 = sm.addPiece(varray2, tarray, to_rgba) > # g2.displayStyle = g2.Mesh > > > to > > # tarray = ((0,1,2),(0,2,3)) > tarray = ((0,1,1),) > # tarray = ((0,1,2),(0,2,3),(0,1,5),(0,5,4),(1,2,6),(1,6,5), > # (2,3,7),(2,7,6),(3,0,4),(3,4,7),(4,5,6),(4,6,7)) > g1 = sm.addPiece(varray, tarray, from_rgba) > g1.displayStyle = g1.Mesh > g1.lineThickness = 3 > > from Matrix import xform_matrix, apply_matrix > tf = xform_matrix(xform) > corners2 = [apply_matrix(tf, p) for p in corners] > varray2 = corners2 > # g2 = sm.addPiece(varray2, tarray, to_rgba) > # g2.displayStyle = g2.Mesh > > Then restart Chimera and use the script you referred to. It will > draw a > line for the axis with width 3 pixels. In the future we will try to > add > some simpler capability to find and show symmetry axes. > > Tom > > > Philip Wurm wrote: >> Hi, >> i have a protein dimer and i would like to show the symmetry axis. I >> found a script in this mailing list: >> >> http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003140.html >> >> which works quite nice. But i would like to have a nicer >> representation >> of my symmetry axis, not this two slabs. Just a line or thin rod >> would >> be nice. >> >> Does anyone know how to do this? >> >> Thanks, >> Philip >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > -- Mark

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Re: [chimera-dev] ViewMatch extension for Chimera
by Eric Pettersen 10 Dec '08

10 Dec '08

> This is my first attempt at writing an extension for Chimera (and > writing anything in python, for that matter). Using the ViewDock > extension as a starting point (which Scooter suggested to me at > CSB2007) made it very easy. There are probably many things that > could be done better. If you have any suggestions, we would very > much like to know. One thing that would be nice to have is to be > able to select a maximum number of matches to load in the ViewMatch > Open-File dialog. Right now, that number is hard-coded in the code, > which is not ideal. First I want to agree with Elaine: ViewMatch is very nice! You can definitely customize Open/Save dialogs to get additional parameters that you need. This is documented in good detail in the module doc string of OpenSave (i.e. at the top of OpenSave/ __init__.py). Basically you: subclass from OpenModeless; supply the 'clientPos' keyword when you call OpenModeless.__init__ from your __init__ (probably with the value 's'); overrride fillInUI() by calling the parent fillInUI() and then populate self.clientArea with your widgets. In your Apply function you would read the values from your widgets (and the file name from self.getPaths()). There's a reasonably simple example of this usage in the AddAttrDialog class in AddAttr/gui.py. You could use the chimera.tkoptions.IntOption widget to get your integer or Pmw.EntryField. You might also like ViewMatch to remember what value the user chose in their last session so you can use it as the widget's default value in the next session. You use Chimera's "preferences" mechanism for that. It's probably easiest to explain by example; here is the prefs.py file of FindHBond: from chimera import preferences BOND_COLOR = 'bondColor' RELAX_COLOR = 'relaxColor' LINE_WIDTH = 'line width' defaults = { BOND_COLOR: (0.0, 0.8, 0.9, 1.0), RELAX_COLOR: (0.95, 0.5, 0.0, 1.0), LINE_WIDTH: 1.0, } prefs = preferences.addCategory("FindHBonds", preferences.HiddenCategory, optDict=defaults.copy()) Basically, the 'prefs' instance can be accessed like a dictionary to fetch the default value of a parameter (prefs[LINE_WIDTH]) or to set a new default (prefs[LINE_WIDTH] = 3) and will be remembered across sessions. I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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patch to bld2vrml for .transparency
by David A. C. Beck 09 Dec '08

09 Dec '08

I've been doing a lot of analysis rendering over proteins in Chimera lately. Bild (via VRML) has worked quite well for this. I wanted the ability to specify a transparency value (from 0 to 1) for the shape objects (boxes, arrows, etc.). The attached patch 'bld2vrml.diff' adds a .transparency 'command' to the bild format that sets the 'transparency' attribute on subsequent objects' 'Material' element in the generated VRML. A sample input file 'test.bild' (see below) and image 'test.png' are also attached. Example input below: .color green .transparency 0.0 .box 5 5 5 10 10 10 .transparency 0.25 .box 0 0 0 5 5 5 .transparency 0.5 .box -5 -5 -5 0 0 0 .transparency 0.75 .box -5 -5 -5 -10 -10 -10 .transparency 0.9 .box -10 -10 -10 -15 -15 -15 -- David A. C. Beck, Ph.D. dacb(a)u.washington.edu Valerie Daggett Laboratory University of Washington, Seattle

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chimera startup problem
by Jinzhong Lin 07 Dec '08

07 Dec '08

Hi, I installed lastest chimera build (1.3.2576) on 32-bit linux platform. When I ran chimera I got following error message Traceback (most recent call last): File "/opt/sciencetools/chimera/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/opt/sciencetools/chimera/share/chimeraInit.py", line 361, in init tkgui.initializeGUI(exitonquit, debug_opengl) File "/opt/sciencetools/chimera/share/chimera/tkgui.py", line 2520, in initializeGUI master.tk.call('tix', 'initstyle') _tkinter.TclError: expected integer but got "9.5" Can anyone help me out? P.S. I opened the tkgui.py file and commented line 2520: master.tk.call('tix', 'initstyle') Chimera start without the error and seems usable, But I am not sure if this is appropriate. Best, lithlin

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Chimera-dev December 2008