- Chimera-users - RBVI Mailing Lists

add atom type in MMTK
by Lionel Nauton 31 May '08

31 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 28 May '08

28 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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