June 2008 - Chimera-users - RBVI Mailing Lists

Installing Chimera in Ubunty Hardy
by David 05 Jun '08

05 Jun '08

Hi, Im a long time user of Chimera, but now I changed XP for Ubuntu for 6 gb of ram that couldn't be used in XP 32 bits. I need help installing Linux version of Chimera, I have read and goggled web for instructions, and none of them seems to work, I run .exe in terminal (knowing linux doesn't use .exe i find this confusing) and nothing happens, I try that Chmod command and running again and nothing too... Im a really beginner here in linux, also browsed Ubuntu forums for help and at least till today have got no answer. All help would be greatly appreciated. sincerely, David Bulnes Abundis

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Chimera - quantitative possibilities using surfnet?
by mgochin＠touro.edu 05 Jun '08

05 Jun '08

I am wondering if it is possible to get numerical values for areas / volumes of molecular cavities and indentations drawn by surfnet in either the Interface or Selected Atoms mode. Any help is appreciated. - Miriam Gochin

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coloring residues according to electrostatic force
by Maurice Ho 05 Jun '08

05 Jun '08

How to color residues of a protein according to the electrostatic potential map generated by APBS? I could only color the molecular surface by loading the potential map. Please kindly advice. Thanks and regards, Maurice Ho

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OS X aqua version
by Glenn Millhauser 03 Jun '08

03 Jun '08

Hi Folks, I just saw the mac aqua version at the download site and decided to give it a try. Layout looks terrific. However, it seems to move molecules much more slowly than the X windows version. I'm running on a macbook (intel) with inherent limited graphics capabilities, so perhaps that's the problem. Any comments? thanks, g Glenn Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 459 2935 fax 831 566 3337 cell glennm(a)chemistry.ucsc.edu http://chemistry.ucsc.edu/~glennm

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making a plane through the atoms of a ring and Distance measurements
by David Chenoweth 03 Jun '08

03 Jun '08

Dear Chimera team, I would like to make a plane through the atoms of an aromatic ring and then measure a distance from an atom to the ring centroid. I would also like to measure the angle between the normal to the ring plane and the line joining the centroid and the atom I am measuring from. It would also be nice if I could specify the dimensions, color, and transparency of the plane. In addition it would be great to be able to make multiple planes through atoms, select and color them separately, and measure the angles at the intersection of the planes. Just wondering if there is a way to do this with Chimera. 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 **********************************************

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fit correlation
by Elena Orlova 03 Jun '08

03 Jun '08

Dear Chimera team, I have some troubles in getting numbers of the quality of the atomic structure fit into EM map. I wonder if you can give me directions where I can find the quantitative assessment of such fit? Do you have something like Cross Correlation Coeficient or R factor, or any other statistical test ? many thanks in advance. Elena -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Elena Orlova Dept. of Crystallography Tel: (+44) (0)20 7631 6845 Birkbeck College Fax: (+44) (0)20 7631 6803 University of London Malet Street London WC1E 7HX UK e-mail: e.orlova(a)mail.cryst.bbk.ac.uk

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Re: [Chimera-users] Chimera-users Digest, Vol 61, Issue 29
by Ibrahim Moustafa 02 Jun '08

02 Jun '08

Dear Chimera developers, Many many thanks for your great help. The script provided by Eric Peterson did the job very easily. Many thanks, Ibrahim On 5/31/08 12:54 PM, "chimera-users-request(a)cgl.ucsf.edu" <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. Re: Plotting modes from PCA onto the structure (Eric Pettersen) > 2. Re: add atom type in MMTK (Elaine Meng) > 3. Import error with chimera-1.2509-osx_x11.dmg, May 01, 2008 > (Bruce D. Ray) > 4. Re: Import error with chimera-1.2509-osx_x11.dmg, May 01, > 2008 (Randy Heiland) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 May 2008 15:15:02 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Plotting modes from PCA onto the > structure > To: Ibrahim Moustafa <I.moustafa(a)psu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <476E9F7A-2FDD-4558-8053-5345D9995A02(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Ibrahim, > As Bala pointed out, IED in VMD may well be the way to go for now. > Also, the "porcupine needles" can be accomplished with BILD, as > Elaine mentioned. I've attached a script that reads a file of > displacements and applies them to the CAs of a structure. Obviously, > there should be as many lines in the file as there are CAs in the > structure. Each line should consist of 3 numbers, the X, Y, and Z > displacements. Since the script only modifies the CAs, you should > probably only be displaying the CAs -- the rest of the structure will > be out of position. You may need to edit the script to put in the > name of the file with the displacements, otherwise it will use a file > named "displacements" in the same directory as the script. You run > the script by simply opening it with File...Open or the "open" command. > We are working on closer coordination between Amber and Chimera, > with the help of Wei Zhang. He has already contributed one tool, > Solvate, which uses sleap to solvate a system. Solvate is available > in daily builds. In the short term he hopes to write tools to add > ions and write parmtop files. Longer term goals are to include the > minimization and MD functionality of NAB, and ptraj trajectory analysis. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > ? > On May 29, 2008, at 10:08 AM, Ibrahim Moustafa wrote: > >> Dear Chimera support, >> >> I hope Chimera (with supporting scripts) can be used to make the >> figures described below: >> >> I want to make a figure to display the different modes >> obtained from PCA analysis (on MD trajectory obtained from AMBER) >> as different snapshots of the structure under study. >> >> To explain it more, I have a file containing the displacement in >> X, Y, Z for each C-alpha in a column format. Is there a simple >> script that can add the displacement vectors to the x, y, z >> coordinates of the original structure? So the new structure with >> modified C-alpha can be plotted representing a particular mode in >> Chimera. >> >> Also, related to the same point, is it possible to represent the >> vectors at each C-alpha as arrows/porcupine needle in Chimera? >> >> P.S. It would be great if Chimera can add features to represent >> these kind of figures from PTRAJ output or similar analysis >> programs used in MD simulation. Especially, Chimera support >> analysis of AMBER trajectory. >> >> Thanks in advance for your great support, >> Ibrahim >> >> >> -- >> Ibrahim M. Moustafa, Ph.D. >> Biochemistry and Molecular Biology Dept. >> 201 Althouse Lab., University Park, >> Pennsylvania State University >> PA 16802 >> >> Tel. (814) 863-8703 >> Fax (814) 865-7927 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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How to define a center of rotation when applying a symmetry
by Giovanni Cardone 02 Jun '08

02 Jun '08

Hi, I would like to apply a rotation to a pdb model, in order to place copies of it in equivalent symmetry points (icosahedral symmetry). I am not sure I understand all the different coordinate systems in chimera, but digging into the program code, I was able to write the following script. I am not sure it is the best way to do it, and obviously at the moment it does not work properly, because I am not specifying the center of rotation. With respect to the coordinates of the pdb model, I know the center of symmetry, let's say (161,161,161), but I don't know how to impose it. I tried to assign these coordinates to the parameter 'cofr', but the result does not change. Does anyone know how to apply, inside a script, a rotation matrix around a given point? Any other feedback on the correctness of the script is very welcome. Thank you. Giovanni ############################################### from chimera import openModels, Point from PDBmatrices import chimera_xform from Icosahedron import icosahedral_symmetry_matrices icomats = icosahedral_symmetry_matrices(orientation = '222r') for rmat in icomats: xf = chimera_xform(rmat) m, = openModels.open('/dummy/dummy.pdb') # open a copy of the model m.openState.xform = xf # set rotation ############################################### ============================================= Giovanni Cardone Laboratory of Structural Biology Research National Institutes of Health 50 South Drive (Building 50), Room 1511 Bethesda, MD 20892-8025 USA Tel: (301) 451-8247 FAX: (301) 480-7629 Giovanni_Cardone(a)nih.gov =============================================

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rotation matrices around a given center (Chimera-users Digest, Vol 62, Issue 3)
by Jonathan Hilmer 02 Jun '08

02 Jun '08

I haven't tried it out, but it looks like all you have to do is apply a transformation to your model before you apply the set of rotations. You could create a set of matrices to do it all in one step, but that's more trouble than it's worth. Something like this should work: Jonathan ############################################### from chimera import openModels from PDBmatrices import chimera_xform from Icosahedron import icosahedral_symmetry_matrices icomats = icosahedral_symmetry_matrices(orientation = '222r') centerRot = (161.,161.,161.) tMat = ((1.0,0.0,0.0,-centerRot[0]), (0.0,1.0,0.0,-centerRot[1]), (0.0,0.0,1.0,-centerRot[2])) for rmat in icomats: m, = openModels.open('/dummy/dummy.pdb') # open a copy of the model m.openState.xform = chimera_xform(tMat) # set translation to for center of rotation offset m.openState.xform = chimera_xform(rmat) # set rotation ############################################### On Mon, Jun 2, 2008 at 1:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > 1. How to define a center of rotation when applying a symmetry > (Giovanni Cardone) > 2. Re: Volume viewer negative isosurface (Elaine Meng) > 3. problem with opengl glx kubuntu (Fabian Glaser) > 4. Re: OS X aqua version (Thomas Goddard) > 5. Re: OS X aqua version (Eric Pettersen) > 6. Re: problem with opengl glx kubuntu (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 Jun 2008 12:18:25 -0400 > From: Giovanni Cardone <cardoneg(a)mail.nih.gov> > Subject: [Chimera-users] How to define a center of rotation when > applying a symmetry > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <919BC0E8-98BD-4F1A-97DD-13F048B71C13(a)mail.nih.gov> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I would like to apply a rotation to a pdb model, in order to place > copies of it in equivalent symmetry points (icosahedral symmetry). > I am not sure I understand all the different coordinate systems in > chimera, but digging into the program code, I was able to write the > following script. > I am not sure it is the best way to do it, and obviously at the > moment it does not work properly, because I am not specifying the > center of rotation. > With respect to the coordinates of the pdb model, I know the center > of symmetry, let's say (161,161,161), but I don't know how to impose it. > I tried to assign these coordinates to the parameter 'cofr', but the > result does not change. > Does anyone know how to apply, inside a script, a rotation matrix > around a given point? > Any other feedback on the correctness of the script is very welcome. > > Thank you. > > Giovanni > > > > ############################################### > > from chimera import openModels, Point > > from PDBmatrices import chimera_xform > > from Icosahedron import icosahedral_symmetry_matrices > > > icomats = icosahedral_symmetry_matrices(orientation = '222r') > > > for rmat in icomats: > > xf = chimera_xform(rmat) > > m, = openModels.open('/dummy/dummy.pdb') # open a copy of the > model > > m.openState.xform = xf # set rotation > > ############################################### > > > > > ============================================= > Giovanni Cardone > Laboratory of Structural Biology Research > National Institutes of Health > 50 South Drive (Building 50), Room 1511 > Bethesda, MD 20892-8025 USA > > Tel: (301) 451-8247 > FAX: (301) 480-7629 > Giovanni_Cardone(a)nih.gov > =============================================

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problem with opengl glx kubuntu
by Fabian Glaser 02 Jun '08

02 Jun '08

Hi, I installed a new version of chimera in kubuntu,and after a while, I started to get the following error when I click chimera: "Missing opengl windowing protocol (glx)" I am using kubuntu version: Linux 2.6.24-16-generic #1 SMP UTC 2008 i686 GNU/Linux nvidia and nvidia-glx are updated and installed. Any help will be highly appreciated. Best, Fabian -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

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Volume viewer negative isosurface
by Miguel Ortiz-Lombardía 02 Jun '08

02 Jun '08

Hi, I'm using Chimera 1.2509 for X11 on a G4 iBook running OSX.4.11 I have a problem with Volume Viewer to visualize an electrostatic potential map calculated with APBS. The same potential map can be used without trouble to color a molecular surface. The problem is that when I try to set a negative isosurface to a negative value, the box that contains map also gets colored, making the scene unclear. I'm attaching a picture to illustrate this effect. I have tried to change several settings but so far unsuccessfully... Thanking you in advance for your help, Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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