- Chimera-dev - RBVI Mailing Lists

alias menu
by Richmond Timothy J. 04 Feb '09

04 Feb '09

Dear Chimera Developers, Perhaps I have missed it, but I would find a menu for selected aliases very useful. Having returned to Chimera from PyMol recently, it would be great to have an option for the alias command that allowed the particular alias to be listed in a separate window and ran the alias by clicking on the alias name listed there. Best regards, Tim ------------------------- ETH Zurich Prof. Timothy J. Richmond Institute of Molecular Biology and Biophysics HPK F 18 Schafmattstr. 20 8093 Zürich SWITZERLAND richmond(a)mol.biol.ethz.ch http://www.mol.biol.ethz.ch/groups/richmond +41 44 633 24 70 phone +41 44 633 11 50 fax

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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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Motivational Posters, Demotivators
by Ean Lay 02 Jan '09

02 Jan '09

Rofl Motivational Posters http://www.roflposters.com

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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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python equivalent for Axis
by Dr. Jean-Didier Maréchal 13 Nov '08

13 Nov '08

Dear all, Sorry to bother you again with a similar kind of question, but I'd like my script to stock in an array the three resulting vectors of the new implemented calculation of the axes for a given set of selected atoms. The truth is that I find the right python call for the axis function. I imported StructMeasure and tried different ways around but I can't find my way through. I don't know if I don't give the wrong arguments or have the wrong syntaxes. Thanks a lot for any help, JD -----Mensaje original----- De: chimera-dev-bounces(a)cgl.ucsf.edu [mailto:chimera-dev-bounces@cgl.ucsf.edu] En nombre de chimera-dev-request(a)cgl.ucsf.edu Enviado el: jueves, 06 de noviembre de 2008 21:00 Para: chimera-dev(a)cgl.ucsf.edu Asunto: Chimera-dev Digest, Vol 58, Issue 2 Send Chimera-dev mailing list submissions to chimera-dev(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev or, via email, send a message with subject or body 'help' to chimera-dev-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-dev-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-dev digest..." Today's Topics: 1. atom spec. in BNF (David A. C. Beck) 2. Re: atom spec. in BNF (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Wed, 5 Nov 2008 14:03:02 -0800 (PST) From: "David A. C. Beck" <dacb(a)u.washington.edu> Subject: [chimera-dev] atom spec. in BNF To: chimera-dev(a)cgl.ucsf.edu Message-ID: <Pine.LNX.4.64.0811051401230.9881(a)homer23.u.washington.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Does anyone have BNF notation for the atom specification 'language' used by Chimera? Thanks, - David -- David A. C. Beck, Ph.D. dacb(a)u.washington.edu Valerie Daggett Laboratory University of Washington, Seattle ------------------------------ Message: 2 Date: Wed, 5 Nov 2008 14:26:16 -0800 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Subject: Re: [chimera-dev] atom spec. in BNF To: "David A. C. Beck" <dacb(a)u.washington.edu> Cc: chimera-dev(a)cgl.ucsf.edu Message-ID: <88F81EBE-CCD4-495F-9316-FEA5D095965D(a)cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii" On Nov 5, 2008, at 2:03 PM, David A. C. Beck wrote: > Does anyone have BNF notation for the atom specification 'language' > used > by Chimera? I don't think so. What's the use case here? If you're in the context of Chimera, you should be able to use Chimera's own atom-spec parsing facilities, e.g. chimera.specifier.evalSpec(). Outside of Chimera, I'm aware of a pretty extensive but not totally complete parser in perl: Chemistry::MidasPattern - Select atoms in macromolecules - search.cpan.org --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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atom spec. in BNF
by David A. C. Beck 05 Nov '08

05 Nov '08

Does anyone have BNF notation for the atom specification 'language' used by Chimera? Thanks, - David -- David A. C. Beck, Ph.D. dacb(a)u.washington.edu Valerie Daggett Laboratory University of Washington, Seattle

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python for finding clashes
by Jean Didier Pie Marechal 29 Oct '08

29 Oct '08

Hi everyone, I am writing a script for which I need the number of clashes for a given selection for continuing. My first thought was to simply run in my script: runCommand("findclash selection ignoreIntraRes false") after having selected the region I was interested in. However, I realize that I come to the recurrent problem: having the information I am interested in printed in the reply log. I don't know how to have the info passed into an array or any kind of variable in the python environment. Could you tell me how to do so please? On the other side, I would be pleased if you could tell me what is the correct arguments I have to pass and syntax I have to use for the functions detectClash and/or cmdDetectClash (which I guess is the basis of the same findclash). All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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

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python for finding clashes
by Jean Didier Pie Marechal 28 Oct '08

28 Oct '08

Hi everyone, I am writing a script for which I need the number of clashes for a given selection for continuing. My first thought was to simply run in my script: runCommand("findclash selection ignoreIntraRes false") after having selected the region I was interested in. However, I realize that I come to the recurrent problem: having the information I am interested in printed in the reply log. I don't know how to have the info passed into an array or any kind of variable in the python environment. Could you tell me how to do so please? On the other side, I would be pleased if you could tell me what is the correct arguments I have to pass and syntax I have to use for the functions detectClash and/or cmdDetectClash (which I guess is the basis of the same findclash). All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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

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Re: [chimera-dev] Chimera-dev Digest, Vol 57, Issue 5
by Patrick Ladam 23 Oct '08

23 Oct '08

>The reason your code did not work is that "ribbonData" is recomputed >whenever the molecule representation is changed (thereby wiping out >your changes). The attribute that actually controls the atoms being >used for ribbon representation is in "ribbonResidueClass" (the name >made sense when I wrote the code :-). Attached is a script that >changes the guide atom for all residues to "C". Please let me know if >you have any questions or suggestions. > >Conrad Hello Conrad, Thank you for your answer and the script, I'll try that right away. Thanks again Patrick

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Changing guide atom - repost
by Patrick Ladam 21 Oct '08

21 Oct '08

Hello list, I received an answer concerning this topic but via the chimera menus which I tested in the first place and works fine. Actually I want to do this from the python shell, so here is my repost: ----------------------------------------------------------------------- I'd like to change the guide atom in res.ribbonData to use C instead of CA as an example. Here is what I did: for r in mol.residues: for a in r.atoms: if a.name == 'C': r.ribbonData.guide = a # Set C as guide Atom if r.isHelix: # Update the display r.ribbonDisplay = True r.ribbonDrawMode = chimera.Residue.Ribbon_Round This does not seem to redisplay/recompute the helix through C Atoms, the helix still goes through CA but not C atoms. I am not confident with the way I altered the guide Atom or maybe is it another problem like updating the ribbon or so... If someone can help... Thanks to all PL

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Bild in python without open/write/close/makecommand ?
by Patrick Ladam 20 Oct '08

20 Oct '08

Hello to all, I have a serie of vectors to draw and update repeatidly. Is it possible to avoid the file open/write/close and makeCommand( 'open myfile.bild' ) process and rather do it in memory within python. In other words, is there a way to interpret bild commands directly in the chimera python module ? Thanks to all Patrick Ladam

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Changing guide atom
by Patrick Ladam 17 Oct '08

17 Oct '08

Hello list, I'd like to change the guide atom in res.ribbonData to use O instead of CA as an example. Here is what I did: for r in mol.residues: for a in r.atoms: if a.name == 'O': r.ribbonData.guide = a # Set O as guide Atom if r.isHelix: # Update the display r.ribbonDisplay = True r.ribbonDrawMode = chimera.Residue.Ribbon_Round This does not seem to redisplay/recompute the helix through O Atoms. I am not confident with the way I altered the guide Atom or is it another problem like updating the ribbon or so... If someone can help... Thanks to all PL

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Problem with sleap II
by Dr. Jean-Didier Maréchal 17 Oct '08

17 Oct '08

Hi guys, I could test again the solvation script. As you said, the problem with the cygwin library is completely solved. I am now running with the following problem: Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmpfqkue6\solvate.cmd (solvate) [gtkleap]$ source leaprc.ff03 (solvate) Error: can not find file leaprc.ff03 in all the search path. Failure running sleap Check reply log for details Thanks for any help, JD *************************************************** Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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

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mixing names
by Patrick Ladam 14 Oct '08

14 Oct '08

Hello to the list, I start trying to write my first py code in chimera (not that easy without too much doc strings) and have a first question to submit. Here is what I am doing in IDLE: >>> import chimera >>> opened = chimera.openModels.open('1zik.pdb') >>> mol = opened[0] >>> for i in mol.atoms: print i.name N CA CB CG CD .../... # Now I want to instanciate an atom and set its name attribute: >>> at1=chimera.Atom >>> at1.name="BC1" >>> print at1.name BC1 >>> # Now I redo the previous loop: >>> for i in mol.atoms: print i.name BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 .../... They're all BC1!!! How come ? My created atom 'at1' and my 'mol' are supposed to be completely seperated objects no? Can someone help, I am afraid I missed something really basic here... Bye to all

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Hydrophobicity
by Leo O'Young 18 Sep '08

18 Sep '08

Hi I am new to the list, I am wondering if it is possible to increase the geometry of the Hydrophobicity-Surface models. Thanks, Leo

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reference guide: long walk off a short pier
by Eric Pettersen 16 Sep '08

16 Sep '08

To reduce the developer's maintenance load, we're looking to shave off parts that don't get much use. One item getting the hairy eyeball is the auto-generated Programmer's Reference Manual pages. Is anyone getting any value from these? If not, we will give them the heave ho. It will also save some on Chimera's download size (800K compressed for download; 21MB on disk). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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chimera import from unmodified python 2.5
by Ondrej Marsalek 12 Sep '08

12 Sep '08

hello everyone, first of all, i would like to say thank you for using vanilla python 2.5, i think this could be quite useful. unfortunately, there is one problem that keeps me from using chimera from a session of my regular python 2.5 installation (on ubuntu 8.04). after setting paths properly, an attempt to import chimera (or the binary module _chimera) produces the following exception: In [1]: import chimera --------------------------------------------------------------------------- <type 'exceptions.ImportError'> Traceback (most recent call last) /home/andy/<ipython console> in <module>() /home/andy/CHIMERA/share/chimera/__init__.py in <module>() <type 'exceptions.ImportError'>: /opt/chimera/lib/libwrappy2.so: undefined symbol: PyUnicodeUCS2_AsUTF8String In [2]: import _chimera --------------------------------------------------------------------------- <type 'exceptions.ImportError'> Traceback (most recent call last) /home/andy/<ipython console> in <module>() <type 'exceptions.ImportError'>: /opt/chimera/lib/libwrappy2.so: undefined symbol: PyUnicodeUCS2_AsUTF8String it seems that the python 2.5 provided with chimera is compiled with different unicode settings than the one in ubuntu. the shared chimera objects are compiled against that version of python and therefore can't be used from my normal python. the only way i see around this at the moment is to recompile chimera, but i wanted to leave that as the very last option. i would appreciate any suggestions, as a straightforward way to use chimera from my normal python would be really neat. i'll be glad to provide details if anyone is interested. regards, ondrej marsalek

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structure analysis feature in UCSF Chimera
by Serge Gorelsky 08 Sep '08

08 Sep '08

Hello, would it be possible to add the two following features to the "Tools/Structure Analysis" menu of UCSF Chimera: the distance between atom A and a plane of other 3 atoms B,C,D ("the height of a trigonal pyramid with atoms B, C, D at the base ") and the angle between an axis (defined by atoms A and B) and the plane B-C-D ? Thank you very much in advance. -- Best regards, Serge Gorelsky (a Chimera user since 2005)

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Re: [chimera-dev] headless chimera issues
by Eric Pettersen 20 Aug '08

20 Aug '08

Hi James, Yes, undoubtedly in nogui mode there is no Reply Log dialog for you to access. If you are using Python, there are far more direct ways to get an atom's coordinates than using getcrd and trying to parse the reply log anyway. Such as: from chimera.selection import OSLSelection sel = OSLSelection("#0:%s.%s@CA" % (snpPos, chain)) a = sel.atoms()[0] crd = a.coord() # or a.xformCoord() for transformed coordinates I've attached a PDF of a handout from a Chimera development class we just taught here at UCSF. It covers a bunch of handy resources and tips. The first resource it lists, the Programmer's Examples, is something you should look over. They cover how Chimera's molecular data is laid out, how to deal with selections, and so forth. --Eric On Aug 20, 2008, at 9:37 AM, James A. Cleland wrote: > Ok, I ran this in chimera (gui) and I see how it is working now, the > reply contains space-separated coordinates at the end of the string > and get_coords picks these off from the end (-1, -2, -3). Perhaps > this is another “headless” issue as there is no dialog? If so, maybe > there’s somewhere else I can pick off the reply information for > getcrd? > > Thanks! > > From: James A. Cleland [mailto:jcleland@jamescleland.com] > Sent: Wednesday, August 20, 2008 12:32 PM > To: 'Eric Pettersen' > Subject: RE: headless chimera issues > > This worked like a charm, thank you! I have run into another issue > that I thought you may be able to help with. > > We are attempting to draw a pointer indicating the alpha carbon for > a particular residue. This has been done in the past, but no longer > works. This may have been something that you helped with. > > The function that is currently failing is called “get_coords()”. > Here’s what I have: > > def _get_coords(): > from chimera import dialogs, Vector > coords = Vector(0,0,0) > r = dialogs.find('reply') > text = r.text.get('1.0', 'end') > coordString = text.splitlines()[-2] > coordString = coordString.split(' ') > print coordString > coords[2] = float(coordString[-1]) > coords[1] = float(coordString[-2]) > coords[0] = float(coordString[-3]) > return cords > > Prior to calling get_coords(), there is a command executed that > seems to provide the dialog information, if I’m understanding > correctly: > > runCommand("getcrd #0:%s.%s@CA" % (snpPos, chain)) > > The line that appears to be failing in get_coords() is the fourth in > the function, r.text.get(). It looks like dialogs.find() returned > None. > > Do you have any suggestions as to how I might get these coordinates > or what we might be doing wrong? > > Thanks! > James > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Tuesday, August 19, 2008 7:41 PM > To: James A. Cleland > Cc: Tom Goddard > Subject: Re: headless chimera issues > > That's right -- the patch just prevents the error. It doesn't do > the coloring. Hopefully Tom Goddard will be able to help you with > that. > > --Eric > > On Aug 19, 2008, at 4:21 PM, James A. Cleland wrote: > > Thank you for the quick reply! I applied this patch manually by just > adding the import and the condition. I had commented the conditional > statements prior to writing you and this worked fine, but the > surface model didn’t appear to be colored according to the Delphi > output. Is it correct for me to assume that, after this patch is > applied, I’m still not seeing the electrostatic potential in the > surface coloring? > > Thanks again, > James > > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Tuesday, August 19, 2008 6:56 PM > To: James A. Cleland > Cc: Tom Goddard > Subject: Re: headless chimera issues > > Hi James, > That exception would be a bug -- SurfaceColor should not > be trying to bring up a dialog if Chimera is running in nogui mode. > I've committed a fix for this and it will be in tomorrow's daily > build. Here's the diff if you want to correct your version: > > *** ChimeraExtension.py 6 May 2008 04:20:05 -0000 1.12 > --- ChimeraExtension.py 19 Aug 2008 22:51:36 -0000 > *************** > *** 50,56 **** > from VolumeViewer import open_volume_file > vlist = open_volume_file(path, ftype, open_models = False, > show_data = False, > show_dialog = False) > ! if len(vlist) > 0: > from SurfaceColor.gui import show_surface_color_dialog > d = show_surface_color_dialog() > d.use_electrostatics_colormap() > --- 50,57 ---- > from VolumeViewer import open_volume_file > vlist = open_volume_file(path, ftype, open_models = False, > show_data = False, > show_dialog = False) > ! import chimera > ! if len(vlist) > 0 and not chimera.nogui: > from SurfaceColor.gui import show_surface_color_dialog > d = show_surface_color_dialog() > d.use_electrostatics_colormap() > > I've cc'ed Tom Goddard on this mail since he is the > expert on Chimera's volumetric API and can hopefully provide advice > on coloring your map programmatically. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Aug 19, 2008, at 1:32 PM, James A. Cleland wrote: > > > Hi Eric, > > My name is James Cleland and I am currently working with Dr. Rachel > Karchin at JHU. I had corresponded with Greg Couch over running > Chimera without an X server and he had directed me toward a build > designed to run headless. I have been using this for a couple of > weeks without problems, but I encountered an issue the other day. > > I am trying to import a surface for electrostatic potential that was > generated using Delphi. The trouble is, this is causing an error > (see below). > > Executing test.py...Opening pdb1a01.ent... > 1 model opened > > Traceback (most recent call last): > File "/home/pipeline/chimera/share/__main__.py", line 65, in > <module> > value = chimeraInit.init(sys.argv) > File "CHIMERA/share/chimeraInit.py", line 384, in init > chimera.openModels.open(a, prefixableType=1) > File "CHIMERA/share/chimera/__init__.py", line 1345, in open > File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython > File "test.py", line 15, in <module> > runCommand("open 1a01.phi") > File "CHIMERA/share/chimera/__init__.py", line 2026, in runCommand > File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand > File "CHIMERA/share/Midas/midas_text.py", line 918, in doOpen > File "<string>", line 1, in <module> > File "CHIMERA/share/Midas/__init__.py", line 1352, in open > File "CHIMERA/share/chimera/__init__.py", line 1345, in open > File "CHIMERA/share/SurfaceColor/ChimeraExtension.py", line 55, in > open_cb > File "CHIMERA/share/SurfaceColor/gui.py", line 613, in > show_surface_color_dialog > File "CHIMERA/share/chimera/dialogs.py", line 77, in display > File "CHIMERA/share/chimera/dialogs.py", line 62, in find > File "CHIMERA/share/chimera/baseDialog.py", line 435, in __init__ > File "CHIMERA/share/chimera/baseDialog.py", line 121, in __init__ > File "CHIMERA/share/chimera/tkgui.py", line 63, in <module> > ImportError: No module named Togl > Error while processing test.py: > ImportError: No module named Togl > (see reply log for Python traceback info) > > From what I can gather, the call to open is trying to present a > dialog for choosing surface colors and limits. I’ve seen this when > running Chimera with an X server. The trouble is, I need to skip > this dialog and, possibly, specify volume in some other fashion. > > We used to use the following python code in our Chimera script: > > from chimera import openModels, MSMSModel > runCommand("set bg_color black") > surf = openModels.list(modelTypes=[MSMSModel])[0] > from VolumeViewer.volume import Volume > vol = openModels.list(modelTypes=[Volume])[0] > from SurfaceColor import color_by_volume > color_by_volume(surf, vol, (-30, 0, 30), ((1,0,0,1.0), (1,1,1,1.0), > (0,0,1,1.0))) > > This was run using an older version of Chimera and used an X server. > We ran into problems using this version with –nogui, which is what > led me to the headless version. > > I have been playing around with SurfaceColor/ChimeraExtensions.py, > specifically line 55-56, trying to figure out how to at least get > color on the surface using the default volume. It appears that, by > commenting the aforementioned lines, I get no surface coloring at all. > > Can you provide some direction for me on this? Any help is > appreciated! > > Thanks, > > James A. Cleland > (w) 1(703)392-1357 > (c) 1(703)402-5447 > jcleland(a)jamescleland.com > > >

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