- Chimera-users - RBVI Mailing Lists

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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Import error with chimera-1.2509-osx_x11.dmg, May 01, 2008
by Bruce D. Ray 31 May '08

31 May '08

I have a Mac G4 PPC running OS X 10.3.9 on which previous versions of chimera have run without incident. I installed chimera-1.2509 of May 01, 2008 after removing the chimera-1.2492 of Feb 11, 2008 I had been using. However, when I attempted to run chimera-1.2509 it did not start and the following error messages were written to the console.log file accessible by console.app rather than to the X-terminal: Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 279, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 15, in <module> from _chimera import * ImportError: dynamic module does not define init function (init_chimera) This appears to be specific to the Mac OS X version as the Windows version of chimera-1.2509 works. Obviously, I removed chimera-1.2509 from the Mac and reinstalled chimera-1.2492 of Feb 11, 2008 which does work on this Mac. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273

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add atom type in MMTK
by Lionel Nauton 30 May '08

30 May '08

hello everybody this is my first question since I use chimera, more than 3 years ago, and I would like to know if is it possible to add atom type in the MMTK basis set ? I actually work on a molecule containing platinium, and I can't run mopac because there is no description. I'm looking for some description files , and I found this : /antechamber/dat/antechamber/*****.DAT which is the good one and which is the way to modify it ? thank's for your answer and excuse me for my english..... best regards -- ================================================= NAUTON Lionel Ingénieur d'études. Laboratoire de Synthèse Et Etude de Systèmes à Intérêt Biologique UMR6504 : université Blaise Pascal – CNRS 24, avenue des Landais – Campus des Cézeaux 63177 AUBIERE Cedex France Tel : 04 73 40 55 06 mèl : lionel.nauton(a)univ-bpclermont.fr <mailto:lionel.nauton@univ-bpclermont.fr> site web : http://seesib.univ-bpclermont.fr/site_web/pageaccueil.htm <http://seesib.univ-bpclermont.fr/site_web/pageaccueil.html> =================================================

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Plotting modes from PCA onto the structure
by Ibrahim Moustafa 30 May '08

30 May '08

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

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Re: [Chimera-users] Chimera-users Digest, Vol 61, Issue 27
by bala 30 May '08

30 May '08

Dear Ibrahim, Try to use IED Plugin in VMD to analyze your PCA output. In fact there is a server that can produce the arrows (you want) that can show the direction and magnitude of the displacement along a Eigen vector. But i guess the server works on gromacs output only. A month ago, i posted the same query to Chimera (Analyzing PCA with chimera). I thank Elaine for his support. I would surely send some samples files of PCA analysis done with PTRAJ. I think addition of this analysis facility in Chimera is surely going to help all chimeran's a lot. Bala -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu on behalf of chimera-users-request(a)cgl.ucsf.edu Sent: Fri 5/30/2008 12:30 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 61, Issue 27 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 modes from PCA onto the structure (Ibrahim Moustafa) 2. Re: Plotting modes from PCA onto the structure (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Thu, 29 May 2008 13:08:01 -0400 From: Ibrahim Moustafa <I.moustafa(a)psu.edu> Subject: [Chimera-users] Plotting modes from PCA onto the structure To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Message-ID: <C4645B32.132A%I.moustafa(a)psu.edu> Content-Type: text/plain; charset="us-ascii" 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

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Help Installing Chimera in Ubunty Hardy already read and google a lot.
by A00775435＠itesm.mx 30 May '08

30 May '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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Re: [Chimera-users] preferences - povray - keep input files doesn't
by Eric Pettersen 27 May '08

27 May '08

> We're thinking of adding some generic per-frame hook as a command so > that you don't have to use Movie Recorder at all to generate a series > of POVray files that you want to post-process before rendering (you > would use the not-yet-documented "export" command to generate them). > > --Eric This hook, a command named "perframe", is now in there. It will be available in tomorrow's build if that works. There is documentation here: http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/midas/perframe.html > > On Mar 17, 2008, at 11:00 AM, Thomas Goddard wrote: > > > Hi Klaas, > > > > You can make the Chimera movie recorder use your preference for > > keeping POVray files by editing file > > > > chimera/share/MovieRecorder/RecorderHandler.py > > > > changing line 120 from > > > > raytraceKeepInput = False, > > > > to > > > > # raytraceKeepInput = False, > > > > Then restart Chimera. > > > > Perhaps we should change the Chimera default for the "keep POVray > > input files" to false and have movie recorder respect the preference > > setting. > > > > Tom > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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H bonds
by Randy Heiland 27 May '08

27 May '08

I have a naive question - given the following pdb file: ATOM 1 CA ALA 0 1.125 1.534 0.000 0.00 0.00 0 C ATOM 2 C ALA 0 0.000 0.514 0.000 0.00 0.00 0 C ATOM 3 O ALA 0 -1.173 0.853 0.000 0.00 0.00 0 O ATOM 4 N ALA 1 0.394 -0.796 0.000 0.00 0.00 0 N ATOM 5 CA ALA 1 -0.546 -1.905 0.000 0.00 0.00 0 C ATOM 6 H1 ALA 1 1.017 2.171 0.880 0.00 0.00 0 H ATOM 7 H2 ALA 1 1.017 2.171 -0.880 0.00 0.00 0 H ATOM 8 H3 ALA 1 1.381 -0.999 0.000 0.00 0.00 0 H ATOM 9 H4 ALA 1 -1.551 -1.486 0.000 0.00 0.00 0 H ATOM 10 H5 ALA 1 -0.420 -2.528 -0.890 0.00 0.00 0 H ATOM 11 H6 ALA 1 2.123 1.091 0.000 0.00 0.00 0 H ATOM 12 H7 ALA 1 -0.420 -2.528 0.890 0.00 0.00 0 H when I display it in Chimera, there are 3 unbonded hydrogens - why is that and is there a menu item to create/display the bonds? thanks, Randy

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povray problem
by Fabian Gmail 27 May '08

27 May '08

Dear chimera team, I have a recurrent problem with the povray facility for saving high quality figures, in many cases I get a black-white figures like the attached. Is there a way to avoid that ? Thanks a lot in advance, 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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Replacing lysine with alanine
by Tom Goddard 23 May '08

23 May '08

Hi Neville, You can replace all lysine residues in a molecule with alanines using the Chimera command swapaa ALA #0:LYS The #0 refers to the molecule id number shown in model panel. Here is further documentation on swapaa. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html Tom yimnai forlemu wrote: > Hi Tom > I have a quick question about chimera. > Can you perform multi amino acid residue mutation > using chimera. For example lets say you have a protein > of 340 amino acids with about 100 lysine, and you want > all the lysines to become say ALaninis. Is that > possible > Thanks > Neville >

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map 3d pdf
by Tom Goddard 23 May '08

23 May '08

Richard Newman wrote: > Hi Tom > > Does CHIMERA have the ability to export a map format which can be used > by 3D PDF? > > We would like to make the EMDB maps available in this format. > > All the best > Richard Hi Richard, Chimera can export map surfaces in several 3-D file formats Wavefront OBJ, POV-Ray, RenderMan, VRML, or X3D using menu entry File / Export Scene.... The format for objects embedded in 3D PDF is called U3D which Chimera does not export. I used a program called MeshLab to read OBJ format produced by Chimera and write U3D format, then used another program to convert LaTeX to PDF (pdflatex). Here's an example showing EMDB map 1356. It requires Adobe Acrobat Reader 8.0. It will not display on Mac OS 10.4 Preview. http://www.cgl.ucsf.edu/home/goddard/temp/emd_1356.pdf Producing the file was painful and Chimera can't export the surface coloring in OBJ format. I think it would be more interesting for the EM Databank to show 3D models in the web browser like JMol shows PDB models. I don't know if a java applet has been written to do that. Perhaps JMol could do it. Tom

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rotate a helix
by Maurice Ho 23 May '08

23 May '08

Hi there, I would like to rotate a helix at a particular angle. How could I accomplish the following? 1. How to define the central axis of the helix in chimera? 2. How to set a particular angle to rotate? 3. I do this on a helix belonging to a GPCR, with the loops firstly broken for rotation and then perhaps need to rejoin them. How to join them back? 4. After joining, should I just redo energy minimization for the loops concerned? Much thanks!

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displacing atoms following a given vector
by Jean-Didier Maréchal 22 May '08

22 May '08

Dear All, I have been flying through the developer's guide but can't find what I look for, sorry. I have a given molecule and a vector in cartesian coordinates (e.g. a normal mode but not necessarily) indicating a direction of displacement for the different atoms of the molecules. I would like to write a script that displaces the atoms following this vector. I am prettysure that some modules of chimera should allow me to do that, but I can't find which ones. Could you give me a hand on this please? ALl the best JD El jue, 22-05-2008 a las 12:00 -0700, chimera-users-request(a)cgl.ucsf.edu escribió: > 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. Stereo projection (Magali Cottevieille) > 2. Stereo projection (Steven Ludtke) > 3. Re: Stereo projection (Greg Couch) > 4. Re: findhbond/5750 (FindHBond failure) (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 21 May 2008 16:06:07 -0400 > From: Magali Cottevieille <mc3077(a)columbia.edu> > Subject: [Chimera-users] Stereo projection > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <483480AF.9020604(a)columbia.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > Is there any way, with two projectors piloted by two graphic cards, to > send from Chimera the stereo left eye view onto one, and the stereo > right eye view onto the other one ? These two projectors are meant to be > used with filters and special glasses to create a 3D view. > Thanks for your help! > > -- > Magali Cottevieille, Ph.D. > Howard Hughes Medical Institute, > Department of Biochemistry and Molecular Biophysics, > 630 W 168th St, P&S Black Building 2-221 > New York, NY 10032 > > Ph: (+1) 212-305-9521 > Fax: (+1) 212-305-9500 > > Email: mc3077(a)columbia.edu > magali.cottevieille(a)gmail.com > > > > ------------------------------ > > Message: 2 > Date: Wed, 21 May 2008 16:18:26 -0500 > From: Steven Ludtke <sludtke(a)bcm.edu> > Subject: [Chimera-users] Stereo projection > To: chimera-users(a)cgl.ucsf.edu > Cc: mc3077(a)columbia.edu > Message-ID: <0F963AC8-7667-4B76-B8E2-0DC9855E406C(a)bcm.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Yes, we have done this before, though I don't remember with absolute > certainty if we > did it with chimera. You don't use 2 video cards normally, but rather > 1 card with 2 > outputs. Also, you will need one of the 'professional' cards where the > driver supports > stereo in a window ie- NVidia Quadro (we didn't try ATI). The NVidea > stereo drivers then > have a mode for this type of stereo, or at least that's my memory, it > was a year or two > ago when we demonstrated this. You need: > > 2 identical projectors which permit geometry correction so their > corners can be exactly aligned > 2 polarizer plates. we got (http://www.3dstereo.com/viewmaster/pj-pfilt-3x3.html > ) for $20 a pair > linear polarizing glasses (from the same site) > Quadro or similar GFX card > > Note that with this type of stereo, you could technically make this > work with any old dual > output 3-D card, but you would have to write the visualization > software so it would open > 2 display windows with slightly different orientations that you could > then manually (or > automatically) position on each of the 2 projectors. > > We did this just as an initial proof of concept, and haven't managed > to get back to it again, > though we keep meaning to, as it is MUCH cheaper than the commercial > solutions. Oh, one warning, > the polarizer plates mentioned above are plastic, and the light energy > put out by your typical > projector is quite substantial. We actually melted one of the > polarizers on our first attempt, > despite using much of it's 3x3 inch surface area. ie - use a low power > projector, or put the > polarizer between thick glass plates or somesuch... > > > From: Magali Cottevieille <mc3077(a)columbia.edu> > > Date: May 21, 2008 3:06:07 PM CDT > > To: chimera-users(a)cgl.ucsf.edu > > Subject: [Chimera-users] Stereo projection > > > > Hi, > > > > Is there any way, with two projectors piloted by two graphic cards, to > > send from Chimera the stereo left eye view onto one, and the stereo > > right eye view onto the other one ? These two projectors are meant > > to be > > used with filters and special glasses to create a 3D view. > > Thanks for your help! > > > > -- > > Magali Cottevieille, Ph.D. > > Howard Hughes Medical Institute, > > Department of Biochemistry and Molecular Biophysics, > > 630 W 168th St, P&S Black Building 2-221 > > New York, NY 10032 > > > > Ph: (+1) 212-305-9521 > > Fax: (+1) 212-305-9500 > > > > Email: mc3077(a)columbia.edu > > magali.cottevieille(a)gmail.com > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > ---------------------------------------------------------------------------- > Steven Ludtke, PhD | Baylor College of Medicine > sludtke(a)bcm.tmc.edu | Associate Professor & Co-Director > stevel(a)alumni.caltech.edu | National Center For Macromolecular > Imaging > V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. > F: (713)798-1625 | > | Those who Do, Are > http://ncmi.bcm.edu/~stevel | The converse also applies > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 21 May 2008 14:25:09 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Stereo projection > To: Magali Cottevieille <mc3077(a)columbia.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0805211409520.1818353(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Wed, 21 May 2008, Magali Cottevieille wrote: > > > Hi, > > > > Is there any way, with two projectors piloted by two graphic cards, to > > send from Chimera the stereo left eye view onto one, and the stereo > > right eye view onto the other one ? These two projectors are meant to be > > used with filters and special glasses to create a 3D view. > > Thanks for your help! > > Chimera supports stereo using workstation graphics cards, i.e., NVidia > Quadro FX and ATI/AMD FireGL cards. We don't have a recent FireGL card > (and driver), so the rest of this email will be about the NVidia Quadro FX > cards and driver. > > The Quadro FX graphics cards have two video outputs and the driver lets > you display the left eye on one output and the right eye on the other. > The higher end cards have SLI support (on FireGL it's called CrossFire) > which lets you use two matched graphics cards together. It is unclear to > me how or if SLI/CrossFire and stereo work together, but I would expect > them to. > > Greg > > > ------------------------------ > > Message: 4 > Date: Thu, 22 May 2008 10:51:29 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] findhbond/5750 (FindHBond failure) > To: Tyler Arbour <tyler.arbour(a)gmail.com> > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <A4A9CFED-F357-4943-AB11-43D644C07DF0(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Tyler, > The problem is that Chimera "knows" the atom types of standard > residues and doesn't try to compute them from scratch. Therefore it > assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the > find-hbond computation as it looks for the planarity of the ND1 and > sees it bonded to nothing! > For what you want to do, you want to get that atom's residue > changed. Do this: > > 1) Control-double click on the ND1 atom > 2) Chose "Modify Atom" from the resulting popup menu. > 3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral" > 4) Change "Bonds" to 3 > 5) In the "Residue Name" section, use the "new residue" option with > "NH3" as the name and chain "het" > 5) Click the Change button > > That should give you what you want. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On May 22, 2008, at 10:25 AM, Tyler Arbour wrote: > > > Wow, I didn't expect a response for this...great! I was actually > > just trying to create a figure representing a computational model > > that I am using. Starting from the crystal structure, I wanted to > > actually change the histidinal N to a simple NH3 molecule. I am > > just trying to get familiar with Chimera--I usually use DS > > Viewerpro for modifying structures, and it doesn't seem like > > Chimera is well-suited to this type of modification. If you have > > any advice on an easy way to make this conversion so that I have a > > nice figure, I'd greatly appreciate it! Thanks. > > > > Tyler > > > > On May 22, 2008, at 11:17 AM, Eric Pettersen wrote: > > > >> Hi Tyler, > >> Your structure seems to have a histidine residue (residue 159 in > >> chain A) that consists solely of an ND1 atom! How did you manage > >> that? > >> > >> --Eric > >> > >> > >> Eric Pettersen > >> UCSF Computer Graphics Lab > >> http://www.cgl.ucsf.edu > >> > >> > > > >

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Re: [Chimera-users] findhbond/5750 (FindHBond failure)
by Eric Pettersen 22 May '08

22 May '08

Hi Tyler, The problem is that Chimera "knows" the atom types of standard residues and doesn't try to compute them from scratch. Therefore it assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the find-hbond computation as it looks for the planarity of the ND1 and sees it bonded to nothing! For what you want to do, you want to get that atom's residue changed. Do this: 1) Control-double click on the ND1 atom 2) Chose "Modify Atom" from the resulting popup menu. 3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral" 4) Change "Bonds" to 3 5) In the "Residue Name" section, use the "new residue" option with "NH3" as the name and chain "het" 5) Click the Change button That should give you what you want. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 22, 2008, at 10:25 AM, Tyler Arbour wrote: > Wow, I didn't expect a response for this...great! I was actually > just trying to create a figure representing a computational model > that I am using. Starting from the crystal structure, I wanted to > actually change the histidinal N to a simple NH3 molecule. I am > just trying to get familiar with Chimera--I usually use DS > Viewerpro for modifying structures, and it doesn't seem like > Chimera is well-suited to this type of modification. If you have > any advice on an easy way to make this conversion so that I have a > nice figure, I'd greatly appreciate it! Thanks. > > Tyler > > On May 22, 2008, at 11:17 AM, Eric Pettersen wrote: > >> Hi Tyler, >> Your structure seems to have a histidine residue (residue 159 in >> chain A) that consists solely of an ND1 atom! How did you manage >> that? >> >> --Eric >> >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >

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Re: [Chimera-users] building linker peptide
by Elaine Meng 22 May '08

22 May '08

On May 21, 2008, at 1:29 AM, Fabian Glaser wrote: > Another question regarding this issue, I succeded to make a new > bond and minimize it between two chains, A and B, in the same pdb. > But this created apparently a problem with the residue numbering > and Nterm recognition, since when I tried to add an additional > linker to the chimera I created, I got the following error message: > > "No MMTK name for atom "H" in standard residue ALA" > > I suspect that this is related to the fact that I still have two > chains, and Chimera does not identified the new bond, or something > similar. > > Is there a way to automatically rename the newly unified chains? > Any suggetion will be highly appreciated. Hi Fabian, There is no automatic way to change chain ID. Only the ugly manual text-editing way, sorry! I guess that the ATOM part of the file no longer agreed with the SEQRES part of the file. It might work to simply delete that atom, if it looks like it is extra. However, I would probably go back to a PDB file saved after you added all your linker residues and edit it to remove all the lines except the coordinates (the ATOM and HETATM lines), remove the chain IDs, and renumber all the residues. It is necessary to renumber the residues because there may be residues with the same number in the different chains, and now there would be no way to tell them apart (for example, two different residues numbered 10, which used to be residue 10 in A and residue 10 in B). Unfortunately you will lose the ability to use the "familiar" residue numbering within the second chain. I attached a fortran (f77) program to do this editing, but I realize you may not be able to use it depending on your computing environment. If you are on some unix-type computer you would just compile it with something like: f77 renum2.f -o renum Then execute it with renum It would ask for the names of the input and output PDB files and what residue number to start with. Then you would have to do the addh/addcharge/minimization stuff again, sorry. I think it would already have the bond you wanted, however. Maybe someone else can think of a more elegant approach. Best, 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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Stereo projection
by Magali Cottevieille 21 May '08

21 May '08

Hi, Is there any way, with two projectors piloted by two graphic cards, to send from Chimera the stereo left eye view onto one, and the stereo right eye view onto the other one ? These two projectors are meant to be used with filters and special glasses to create a 3D view. Thanks for your help! -- Magali Cottevieille, Ph.D. Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, 630 W 168th St, P&S Black Building 2-221 New York, NY 10032 Ph: (+1) 212-305-9521 Fax: (+1) 212-305-9500 Email: mc3077(a)columbia.edu magali.cottevieille(a)gmail.com

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Stereo projection
by Steven Ludtke 21 May '08

21 May '08

Yes, we have done this before, though I don't remember with absolute certainty if we did it with chimera. You don't use 2 video cards normally, but rather 1 card with 2 outputs. Also, you will need one of the 'professional' cards where the driver supports stereo in a window ie- NVidia Quadro (we didn't try ATI). The NVidea stereo drivers then have a mode for this type of stereo, or at least that's my memory, it was a year or two ago when we demonstrated this. You need: 2 identical projectors which permit geometry correction so their corners can be exactly aligned 2 polarizer plates. we got (http://www.3dstereo.com/viewmaster/pj-pfilt-3x3.html ) for $20 a pair linear polarizing glasses (from the same site) Quadro or similar GFX card Note that with this type of stereo, you could technically make this work with any old dual output 3-D card, but you would have to write the visualization software so it would open 2 display windows with slightly different orientations that you could then manually (or automatically) position on each of the 2 projectors. We did this just as an initial proof of concept, and haven't managed to get back to it again, though we keep meaning to, as it is MUCH cheaper than the commercial solutions. Oh, one warning, the polarizer plates mentioned above are plastic, and the light energy put out by your typical projector is quite substantial. We actually melted one of the polarizers on our first attempt, despite using much of it's 3x3 inch surface area. ie - use a low power projector, or put the polarizer between thick glass plates or somesuch... > From: Magali Cottevieille <mc3077(a)columbia.edu> > Date: May 21, 2008 3:06:07 PM CDT > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Stereo projection > > Hi, > > Is there any way, with two projectors piloted by two graphic cards, to > send from Chimera the stereo left eye view onto one, and the stereo > right eye view onto the other one ? These two projectors are meant > to be > used with filters and special glasses to create a 3D view. > Thanks for your help! > > -- > Magali Cottevieille, Ph.D. > Howard Hughes Medical Institute, > Department of Biochemistry and Molecular Biophysics, > 630 W 168th St, P&S Black Building 2-221 > New York, NY 10032 > > Ph: (+1) 212-305-9521 > Fax: (+1) 212-305-9500 > > Email: mc3077(a)columbia.edu > magali.cottevieille(a)gmail.com > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Associate Professor & Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. F: (713)798-1625 | | Those who Do, Are http://ncmi.bcm.edu/~stevel | The converse also applies

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Re: [Chimera-users] Low resolution surface model
by Elaine Meng 21 May '08

21 May '08

On May 20, 2008, at 10:21 PM, Damien Larivière wrote: > Dear Elaine, > Here is what I would like to do with Chimera : > > From Tools/Structure analysis/sequence, it is possible to copy a > portion of the aminoacid sequence of a protein and then to > highlight in an other color this portion of sequence in a high > resolution surface model (Actions / surface / show). > > I would like to highlight a given portion of sequence but in a low > resolution surface model. I tried High-Order Structure / Multiscale > models with no success. > > Thanks for you help and congratulations for the work you perform. > Damien > ------------------------------------------ > Damien Larivière > Fourmentin-Guilbert Scientific Foundation > 2 Av. du Pavé Neuf, 93160 Noisy-le-Grand, France > Phone : + 33 1 43 03 06 20 > Cell phone : +33 6 82 19 81 32 > damien.lariviere(a)fourmentinguilbert.org > Hi Damien, You can color a low-resolution surface for certain residues, but it takes an additional step as compared to coloring the high-resolution surface. Another difference is that it is done by distance cutoff, because it is no longer clear exactly which atom goes with which point on the surface. (1) First create the low-resolution surface. I can think of two different ways: (a) Multiscale Models - click "Make Models" and that will create a separate low-res surface for each chain. In that dialog, if you select "All" chains you can then edit the resolution value for those surfaces. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ framemulti.html (b) command "molmap" - it makes a density map from the atomic coordinates, which you can then display as an isosurface. The Volume Viewer tool is automatically opened to show the density; in that tool, you can drag a bar on the histogram to change the contour level. In this case, all the atoms in the structure are used, and so you would get one "blob" (depending on contour level, though) rather than separate surfaces per chain. Volume Viewer has many additional options including surface smoothing (see Features... Surface and Mesh options). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ framevolumeviewer.html (2) Select the residues and perform the coloring. This can be done exactly the same as for the high-resolution surface, and there are many different ways. To select the residues, you can use the Sequence tool (as you described), or the Select menu, or commands; to perform the coloring, you can use Actions...Color or the "color" command. However, the low-res surface will not be colored yet... (3) Use Color Zone (under Tools.... Volume Data) to color the surface to match the atoms you just colored. This just uses a simple distance cutoff and colors parts of the surface to match the closest atoms. After clicking Color, you can just drag the slider to change the distance cutoff. You're welcome! I hope this helps, Elaine P.S. we are working on better integration of different kinds of surfaces, so this procedure may change in the future ----- 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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reporting sigma values for electron density maps
by David Chenoweth 20 May '08

20 May '08

Hi! Can you please let me know if there is a way to report or set the sigma value for an electron density map from a high resolution crystal structure. I am using a ccp4 FWT.map and DELFWT.map file for structures <1.2 angstrom resolution. Can I somehow find the sigma value that corresponds to the Level setting in the Volume viewer? Thanks, Dave Chenoweth ********************************************** 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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saving multiple maps
by odonnell＠chem.fsu.edu 19 May '08

19 May '08

Similar to saving multiple PDB's as a single PDB file, is there a way to save multiple maps (e.g mrc or ccp4) as a single map file. Thanks in advance for anything which could help me out!! -Jason ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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building linker peptide
by Fabian Gmail 18 May '08

18 May '08

Dear Chimera experts, I am willing to build a peptide "linker" connecting two different pdb chains, that is to connect two existing pdb chains with a new peptide chain, and if possible minimize it. Is it possible to do that wich chimera? I know the command addaa, but to my best understanding this command it's not able to connect the end of the new peptide with the beginning of the second chain. Any suggestions will be greatly appreciated. Best regards and thanks a lot in advance, 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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Action focus
by Thomas Goddard 15 May '08

15 May '08

I made Action / Focus work on selected surfaces. Also I made the none-implies-all rule include surfaces in the "all". So Actions / Color / green will color everything green including surfaces if nothing is selected. I fear this a bit because volume user often have tens of maps and pdb models open and could shoot themselves in the foot pretty easily. These changes were a bit more complicated than expected and may be a buggy. Report anything suspicious or wait until next week when I shake it down a bit more. Tom

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electrostatic potential colored surfaces script
by Miguel Ortiz-Lombardía 15 May '08

15 May '08

Dear all, I wonder if someone has written and would share a script to sequentially read a pdb file, show its molecular surface and color it by the electrostatic potential from an appropriate .dx file. Cheers, 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

2 2

Help needed
by Bagchi, Angshuman 13 May '08

13 May '08

Hi, I am a student of IUPUI (indiana-University-Purdue University-Indianapolis). I would like to know how chimera can be used to select the amino acid residues of one chain of a protein, which are within a certain distance (say 10A) of another chain of the same protein. For example, the pdb 1o6s has two chains A and B. I would like to find what amino acid residues of A chain of 1o6s are within 10A of B chain of 1o6s. I am eagerly expecting a reply from your end. Thanks Ang

3 2

Drawing a circle or square
by Elaine Meng 12 May '08

12 May '08

Hi Pradeep, Other people have recommended Adobe Illustrator and Inkscape for such purposes: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-April/002579.html However, you CAN draw a rectangle in the BILD format and read that into Chimera. For example, put the following 7 lines in a text file named square.bild and open it with File... Open: .scale 1.5 .color red .move 0 0 0 .draw 5 0 0 .draw 5 5 0 .draw 0 5 0 .draw 0 0 0 I also attach said file below, for your convenience. You can edit the coordinates, scale, and color. Once you open it in Chimera, it is a separate model, and you can move it independently using the checkboxes below the Command Line or the "Active" checkboxes in the Model Panel. Advantage: since it does exist in 3D, you can place it between the surface and the nucleic acid. Disadvantage: cannot make curves/circles, may be hard to position/orient, cannot control line thickness. The thickness issue may be addressed by instead making the edges cylinders and the corners balls. This can also be done in the simple BILD format, but it is sort of a hack to make a 3D object when you really want a 2D object. BILD format description: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html I hope this helps, 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 On Apr 30, 2008, at 11:57 AM, Pallan, Pradeep S wrote: > Hi Elaine, > I am wondering whether one can draw a circle or a square > to indicate a site/s of a protein? Attached is a tiff file that has a > square and a circle. I want the regions to be pointed out. > > So what I did: > 1) Generated the image in chimera > 2) added a circle and a square in microsoft paint (Doesn't look > good!). > > I was going through the chimera tutorials, but didn't find the > feature. > Any suggestions for adding a circle or square? In my case, the > surface image is at the back, and nucleic acid in the front. > I would like to draw the circle and square and then load the nucleic > acids, so that will look better. In other words the square or > circle in > between > the surface image (at the back) and the nucleic acid (in front). > > If editing the tiff file using Adobe photoshop (instead of MS paint) > it does a better job, thick lines etc, but it leaves patches on the > nucleic > acid. > I appreciate your help. > Thanks, > Pradeep

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measure volume area request
by Tom Goddard 12 May '08

12 May '08

Edward Brignole wrote: > Tom, > > I have a request for display of the measure volume area tool - can it > be moved from "tools" to "features" such that it is displayed in the > volume viewer along with color, voxel size, etc. The problem I have > is that frequently I have 30 or so volumes to open at once and then > need to independently go through them and set density thresholds. > It's really a pain to have to select the volume once in the volume > viewer and then again select the same volume in the measure tool then > go back to the viewer and adjust threshold. After doing this 30 > times, you'll find that most of the effort is spent making sure to > select the same volume in both menus so that the selected volume that > you are adjusting is the same volume being measured. > > Thankfully, I did however find a python script that you emailed a year > ago that I can steal a few lines out of to adjust the thresholds > automatically so that the enclosed surface of each model has the > appropriate volume in A^3. BTW, I really like your hidedust.py as > well, however once I've executed that script adjusting the threshold > in the volume viewer does nothing to the displayed or measured volumes > - I'm using the snapshot from a week or so ago. > > Ed > > Ed Brignole > Asturias Lab, CB227 > The Scripps Research Institute > Hi Ed, I agree it would be helpful to have a measured volume/area panel in the volume dialog. I'll add that to our requested features list. http://www.cgl.ucsf.edu/chimera/plans.html It still needs to be a separate dialog too because it works on surfaces that are not from volume data (e.g. molecular surfaces). The hidedust.py script hides connected components smaller than a specified volume. But the Measure Volume and Area dialog displays values for the entire surface, hidden or not. So those values don't change. Currently there is no provision in the volume/area measurement to exclude the hidden part of the surface. You also say that changing the contour level does not change the displayed surface. As soon as you change the contour level the whole surface is replaced. The hidedust.py script only acts on the surface that is shown at the time you run it, not on future surfaces, so all the dust should come back. You seem to say this is not what happens in your use. I've attached the hidedust.py script to this email in case you are using a different version. Tom # ----------------------------------------------------------------------------- # Hide connected components of a surface with small enclosed volume. # # Tested with Chimera version 1.2500. Will not work with 1.2470 or earlier. # def hide_small_blobs(p, volume): varray, tarray = p.geometry from numpy import ones, intc mask = ones((len(varray),), intc) from _surface import connected_pieces cplist = connected_pieces(tarray) hid = 0 for vi, ti in cplist: ta = tarray.take(ti, axis = 0) from MeasureVolume import enclosed_volume vol, holes = enclosed_volume(varray, ta) if not vol is None and vol < volume: mask.put(vi, 0) hid += 1 p.setTriangleMaskFromVertexMask(mask) print ('Hid %d of %d connected surface components having volume < %.5g' % (hid, len(cplist), volume)) # ----------------------------------------------------------------------------- # Return all surface pieces if none are selected. # def selected_surface_pieces(): import Surface plist = Surface.selected_surface_pieces() if len(plist) > 0: return plist from chimera import openModels from _surface import SurfaceModel plist = [] for m in openModels.list(modelTypes = [SurfaceModel]): plist.extend(m.surfacePieces) return plist # ----------------------------------------------------------------------------- # volume = 100.0 for p in selected_surface_pieces(): hide_small_blobs(p, volume)

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Encoding movie by hand
by Tom Goddard 12 May '08

12 May '08

Anindito Sen wrote: > > Hi Tom > > How can we make a movie (not morphing) out of several still snaps > (.jpg) saved from of many density maps. > using chimera. > > Thanks > qandy > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908 Hi Qandy, You can create a movie directly from a set of images using the ffmpeg executable included in the Chimera distribution. When you make a movie using Chimera it runs the ffmpeg executable to make the movie file and the options used are printed to the Chimera reply log (Favorites / Reply Log). For example, in the reply log I see ARG_LIST IS ['-r', '25', '-i', '/tmp/chimovie_JgKl-%05d.ppm', '-y', '-f', 'mov', '-b', '2000', '-bufsize', '200', '/Users/goddard/chimera_movie.mov'] Movie saved to /Users/goddard/chimera_movie.mov so the ffmpeg command used was: ffmpeg -r 25 -i /tmp/chimovie_JgK1-%05d.ppm -y -f mov -b 2000 -bufsize 200 You could run a similar command from a shell to encode a movie outside of Chimera. The files are specified by the "-i" option. In the example they are ppm format but jpg will work too. The %05d means that the file names ended in a 5-digit number with leading zeros (e.g. chimovie_JgK1-00000.ppm, chimovie_JgK1-00001.ppm, ...). The -r option indicates frame rate (25 frames per second). The -f option is output format (mov = quicktime). The -b option is bit rate (Kbits/sec) and controls output quality. The -y option means to overwrite the output file if it already exists. For complete ffmpeg options see online docs: http://ffmpeg.mplayerhq.hu/ffmpeg-doc.html The Chimera copy of ffmpeg is in the distribution in chimera/bin (or on Mac in Chimera.app/Contents/Resources/bin). Tom

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Program won't open
by Abigail Lambert 12 May '08

12 May '08

Hello - I'm using a MacBook Pro, OS X (10.4.11), and I had been successfully using Chimera for a while. Then all of sudden, the program will no longer open. The Chimera icon blinks once in the taskbar, and then it disappears and the program does NOT open. I tried uninstalling and re-installing, but this does not help. Any suggestions? Thanks! - Abbie -

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Renaming chains in a PDB file with two chains
by Harinathachari Bahudhanapati 10 May '08

10 May '08

Hi Elaine, Thanks for all the answers you give to our questions. They are very helpful as I learn more everyday. I have a question. Is there anyway to rename a chain in a PDB file through the GUI? I have a few PATCHDOCK generated PDB files with two different chains named under Chain 'A' as #0.1 and #0.2. When I try to get the list of hydrogen bonds between these two chains, the chain name 'A' appears for all of the h-bonding pairs. So, I want to have them named Chain A and Chain B for easier analysis than scratching my head figuring out which h-bond pair is between the chains or with in the chain. I am attaching the pdb file. Please help me. (I thought of renaming the chains in the PDB file going through the PDB header (text file) and manually changing the name. But I am not a expert if anything goes wrong.) Sincerely Hari

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Dashed H-bond
by Ibrahim Moustafa 09 May '08

09 May '08

Dear Chimera Team, Few weeks ago I asked about how to make H-bonds with dashed line style, I got your great help in that. So, I can make the H-bond with the color and style I want; however, when saving the image (with POV true) I got the H-bond appeared with the new chosen color but not as dashed line shown in the display. But, if I save the image with POVray option false, I got the same style shown in the display (new color and dashed line). The question is why saving the image using ³POV true² does not give the image as it appears in the display? Again, it accepts the new color but not the dashed style. Thanks for your great help, 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

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Number of voxels?
by Kolodziej, Steven J 09 May '08

09 May '08

I was wondering if anyone knows how to tell how many voxels within a bounding box can be assigned to protein signal instead of "empty space" at any given contour/density level? Thanks, Steve Kolodziej

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saving a stereo image
by Elaine Meng 09 May '08

09 May '08

On May 9, 2008, at 9:04 AM, Pallan, Pradeep S wrote: > > Hi Elaine, > I am trying to save a generate a stereo image by following the > instructions: > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ > frameimages.html > > I captured left eye and right eye images separately, pasted > them side by side ~65 mm apart, and I see this do not appear as > stereo. Any comments and instructions? I can send you the image > if you want to take a look at it. > > Thank you very much, > Pradeep Pallan Hi Pradeep, I think you are looking at old documentation. I don't think the current documentation says anything about saving separate images for left eye and right eye. This is the current page: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/ print.html#stereo Here is the blurb from that page, but it is probably better to go to the URL because there are helpful hyperlinks: Stereo. Wall-eye, cross-eye, and red-cyan stereo images can be saved by changing the graphics window to the corresponding camera mode with the Camera tool (or the command stereo) and using the "same as screen" Image camera mode in the Save Image dialog. Another way to save cross-eye stereo images is with the "stereo pair" Image camera mode; in that case, it does not matter what camera mode is being used in the graphics window, but the resulting image will be twice as wide as the specified size. Those approaches should work, assuming you also have a recent version of Chimera! (last production release Nov 2007 or newer) Best, 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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Selected residues already shown on the screen
by Ibrahim Moustafa 08 May '08

08 May '08

Dear Chimera team, How to include residues previously selected and shown on the screen with a new selection? For example, I did a selection for few residues and displayed them on the screen; then removed the selection. I wanted to run hbond on those residues already on display. How to do that? Thanks, 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

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MemoryError restoring session
by Eric Pettersen 07 May '08

07 May '08

Christian Rickert wrote: > At the university, I saved a huge project of mine containing a > density map and multiple (!) rigid-body fitted pdbs. > Although this system is a 32-bit Kubuntu 8.04 only (4 Gig of RAM > installed), I observed the same problems with my 64-bit SUSE 10.3 > (4 Gig of RAM installed as well) at work. > > Creating this project took me two days in total, so I really would > appreciate any suggestions from you ... Hi Christian, It's possible that your shell is imposing a limit on memory use by a single process. Before starting Chimera, remove the memory limit of your shell by typing: csh-type shell: unlimit sh-type shell: ulimit -v unlimited Let me know if this helps or not. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to use hbonds spec
by Miguel Ortiz-Lombardía 07 May '08

07 May '08

Hello, I'm trying to follow hydrogen bonds in a trajectory from amber. To do so, I would like to run a 'per frame' script with something like: hbonds spec :100 selRestrict cross relax false However, this fails because apparently no atoms are selected. This fails as well: hbonds spec #0:100 selRestrict cross relax false I can only see the hydrogen bonds if insert a select :100 before the hbonds command. I wouldn't like to see the green 'aura' of the selection, that's why I would like to make the selection within the hbonds command. I'm probably missing something, but cannot figure out what. Thank you! 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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Tile structure request
by Eduardo Sanz-Garcia 06 May '08

06 May '08

I noticed that the tile structure option arranges the models logically when there are 5 or less models opened. When there are 6 or more, the arrangement is a little bit chaotic, the models are not placed sequentially. Could this option be improved so the sequence is more logical? Thank you very much. Chimera is great!! PS: I am used to work with EM models, I don't know if the previously described behaviour also applies to atomic coordinates models.

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solvent-accessible surface area
by Elaine Meng 06 May '08

06 May '08

Dear Jose, Prof. Ferrin forwarded your question to me. Our program Chimera, the successor to MidasPlus, can calculate the solvent-accessible surface area. It is available for download for Windows, Mac OSX, Linux and other platforms. The features I will mention are relatively new, so you would need to get a recent version such as the May 1 snapshot: http://www.cgl.ucsf.edu/chimera/download.html#snapshots You would first load the structure in Chimera (File... Open for a local file, File... Fetch by ID to get it directly from the PDB). Then there are a couple of different approaches you could take. (1) simply show a molecular surface in Chimera (Actions... Surface... show) or command "surface". The total will be reported in the Reply Log (under Favorites in the menu). You can use the solvent- accessible value or solvent-excluded as you prefer. The difference is explained here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces Besides the total, the values per atom and per residue are assigned as "attributes" named areaSAS and areaSES for solvent-accessible and solvent-excluded, respectively. You can see a histogram of the values by opening "Render by Attribute" (under Tools... Depiction), and you can write out the values to a file by choosing File... Save Attributes from that dialog's menu. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#render The Render dialog can be set to show the values for "atoms" or "residues" (simply the sum over the atoms in each residue). What it writes out are the atom (or residue) specifiers and the value for each, not a grid. (2) instead of doing the calculation in Chimera, you can send the coordinates to a web server with the tool "Area/Volume from Web" (under Tools... Surface/Binding Analysis). There are various options for what you want to calculate. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html Again you get the values assigned as attributes (but this time atoms only) and can view and save them in the same way as described for #1 above. The help links above are part of the User's Guide, which is also accessible from the Help menu of Chimera, once you have downloaded it (Help... User's Guide, Search Documentation, Tutorials). If you still have trouble you can send questions to chimera-users(a)cgl.ucsf.edu I hope this helps, 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 On May 5, 2008, at 4:52 PM, Tom Ferrin wrote: > ------- Forwarded Message > > Date: Wed, 30 Apr 2008 17:20:27 -0400 > From: Jose Gascon <jose.gascon(a)uconn.edu> > To: tef(a)cgl.ucsf.edu > Subject: midasplus > > Dear Prof. Ferrin > > I am an Assistant Professor in the Chemistry Department at UConn, I am > interested in calculating the solvent accessible area of a protein. I > looked up on the internet and found that the program midasplus is > suppose to do that. The links seem to be outdated and I was not been > able to find the program. I assume that midasplus has probably evolved > to other programs such as chimera. I understand that you were involved > in the development of this program. > > At the end, given a pdb input file, I am just interested in > obtaining a > grid of x,y,z coordinates representing the SAS. > Do you know if there is such a program? Is DMS, from midasplus, still > available somewhere? > > Thanks for your help. > > Sincerely, > > Jose A. Gascon > > > -- > Jose A. Gascon - Assistant Professor > 55 North Eagleville Rd. > Department of Chemistry > University of Connecticut - (860) 486-0591 > Storrs, CT 06269 > http://gascon.chem.uconn.edu > > ------- End of Forwarded Message >

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movie trajectory
by Jean-Paul Armache 05 May '08

05 May '08

Hi Elaine, Eric, Thanks for the answer - I know the webpage for the movies, but it will be helpful to use the savepos command. I will let you know whether this produces the desired effect or further help will be needed. Best regards, Jean-Paul

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movie trajectory
by Jean-Paul Armache 05 May '08

05 May '08

hi all, i have a small question. would any of you know a way to set up a specific trajectory for a camera to move around the molecule? i know you can rotate the whole molecule, but the question is more related to similarity to 3ds max or maya - if you could set up a specific way the camera moves around the molecule (rotation, movement at specific point, zoom, stop, restart, further movement etc) ? maybe the question is trivial, however i haven't found a way to do it (an easy way - you can do quite a huge script with small movements - one step at a time). my question is more about path drawing and setting stop points. regards, jean-paul

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Re: [Chimera-users] transparent surfaces (fwd)
by Greg Couch 05 May '08

05 May '08

Just so everyone on the list knows. Extrapolating from what Charles said, the error was probably that MegaPOV wasn't able to include the transforms.inc file because MegaPOV wasn't configured properly to include the POV-Ray library files. And on Mac OS X, Linux, and other UNIX systems, to use the CHIMERA/bin/povray.exe program outside of chimera, you need to setup the shared library path to include CHIMERA/lib. Chimera does that setup automatically for many of the programs in CHIMERA/bin, so we should probably fix it for povray as well, but if you're going to use your own POV-Ray anyway, like the multi-threaded 3.7 beta release, then that is not an issue. - Greg ---------- Forwarded message ---------- I figured it out. In MegaPOV you need to set the library path for the render, also POVray 3.6 will not work as a standalone application in Mac OS 10.4 and higher. Charles On May 5, 2008, at 2:15 PM, Greg Couch wrote: > On Thu, 1 May 2008, Charles Midgett wrote: > >> I want to make a transparent surface in volume viewer that can be >> drawn in POVray. It appears the *.pov and *.ini files produced by >> Chimera cannot be read by other POVray renders. Is there some work >> around that will allow me to ray trace a transparent surface >> displayed by the volume viewer? >> >> Charles > > That is news to us. The chimera povray output was only tested with the > POV-Ray 3.6.1 renderer that comes with chimera. Please submit a bug report > using chimera's Help / Report a Bug dialog and include the name and version > number of the other POV-ray renderers, as well as the error message you get. > > Thank you, > > Greg Couch > UCSF Computer Graphics Lab

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Consistency of surface color
by Bui Khanh Huy 05 May '08

05 May '08

Hi all, I have a problem with color consistency on Chimera. The surface color of my model from my Windows server is different than that from my linux server. Even when I connect from home to the linux server, the color render is also different from those two above. I use the same session for all of them but the color comes out quite different on different machines. Is there anyway to avoid this inconsistency? Regards, Huy

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