June 2009 - Chimera-users - RBVI Mailing Lists

high quality pictures for publication
by Fabian Glaser 25 Jun '09

25 Jun '09

Hi all, I am trying to produce high quality figures for publication with chimera, and despite I am working some time with it, I am not quite satisfied with the result I get. I don't know if I can send figures to this list, just as example I send these two. They are fine, but they are not gorgeus as I would like. I don't know they are produced with and without the pov-ray in linux, with 300 dpi, etc. Could somebody try to help me how to improve them? 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

3 4

Re: [Chimera-users] Surface Creation
by Eric Pettersen 23 Jun '09

23 Jun '09

On Jun 23, 2009, at 2:25 PM, Thiruvarangan Ramaraj wrote: > Hi, > > I tried to create two surfaces, one for the Antibody and one for the > Antigen for an Antibody-Antigen complex (1A14.pdb). I am able to > create two surfaces as two models in one session. But when I try to > save this session it gives me an warning > "Cannot save surfaces without associated structure. > Surface will not be saved." This happens when you close the structure that a surface is based on. Sessions don't store vertex/triangle information for surfaces (which would be voluminous) but instead just the parameters that were used to generate the surface -- and the surface is regenerated when the session is restored. But if the underlying structure is gone then that won't work. > Then when I try to open the saved session there is only surface that > I could see. > > Is there any way that I could have both surfaces saved in one session. > > Any help would be greatly appreciated. Well, obviously one approach is to not close the underlying structure. FYI, you can get separate surfaces on the antigen/antibody without using multiple copies of the structure. You need to get the antigen and antibody into separate "surface categories" (as described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/msms.html ). Here is a sequence of commands (Favorites->Command Line) that gets the antigen (chain N) into its own surface category named "antigen" and then surfaces both the antigen and antibody: surfcat antigen :.n; surf antigen; surf --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Saving image and rendering
by Ibrahim Moustafa 23 Jun '09

23 Jun '09

Dear Chimera team, Recently, I have some trouble saving images with POV-RAY option ³true². The process of rendering is too slow (both on the mac and windows version). To give the feeling of how slow: rendering an image with 1700 lines takes 7 hrs (with quality 9 in pov-ray options) and 2 hrs (quality 5). I used to get the images rendered much faster than that (with older versions; however, I¹m not exactly sure of when I started to see such a slow rendering behavior). There is another related problem but only with the windows version: If I want to save an image, with depth cue, using the fast mode (POV-RAY false), the image output lacks any depth used in the model, with poor quality and darker than it should be. Somehow, the camera orientation is messed. In addition, the depth cue will be no longer available for the rest of the session (I have to restart over again). To get the depth cue I want, I need to turn the POV-RAY option ³true²....but then too slow to create a good figure. I¹d appreciate any comment or explanation from Chimera people; and what is the best way to overcome this problem? P.S. I have the PPC version for the MAC running OSX 10.4; the PC running Windows XP. Many thanks in advance for your 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

4 5

New surface coloring command
by Thomas Goddard 22 Jun '09

22 Jun '09

I added a Chimera command "scolor" that can color surfaces radially or according to volume data values such as electrostatic potential. This command is the equivalent of the Surface Color dialog. A few examples: scolor #0 geometry cylindrical colors the surface by distance from a cylinder axis (default z-axis) with default coloring red-white-blue ranging from minimum to maximum surface radius. scolor #0 geom radial cmap 100,gray:150,blue:200,purple colors radially with colors gray,blue,purple at radii of 100,150,200. scolor #0 volume #1 cmap -10,red:0,white:10,blue colors surface #0 using volume data #1 with colors red,white,blue for volume data values -10,0,10. Here's a summary of the full command syntax. Detailed documentation will be available in the manual before the next Chimera release. scolor <surfaceSpec> [volume <vspec>] [gradient <vspec>] [geometry radial|cylindrical|height] [color <color>] [center <x,y,z>|<atomspec>] [axis x|y|z|<x,y,z>|<atomspec,atomspec>] [coordinateSystem <modelid>] [cmap <v,color>:<v,color>:...|rainbow|gray|redblue|cyanmaroon] [cmapRange <min,max>|full] [reverseColors true|false] [colorOutsideVolume <color>] [autoUpdate true|false] [capOnly true|false] [perPixel true|false] Tom

1 0

Getting Delphi
by Yasser Almeida Hernandez 22 Jun '09

22 Jun '09

Hi all... Where can i download the Delphi executable to run in Chimera...? Thanks ---------------------------------------------------------------- Correo FENHI

2 1

Electrostatics
by Gawronski, Alexander 20 Jun '09

20 Jun '09

Hello, I'm a student at Carleton University and I need to create meshes with electrostatic coloring for all the proteins in the pdb. I need a way of automating this process with scripts but I can't figure out how. Is this possible to do this through command line? How do I call chimera commands from a script? Any help would be greatly appreciated! Thanks, Alex Gawronski

4 3

Re: [Chimera-users] 3D mouse - connexion
by Nils Becker 18 Jun '09

18 Jun '09

Hi Thomas, I'm also using it (recently, on a daily basis, on Mac OS X). It works very nicely, and it's cheap. Also, try the keyboard shortcuts na, nz etc... cheers, Nils

1 0

3D mouse - connexion
by Thomas C. Marlovits 18 Jun '09

18 Jun '09

Hi, the Chimera documentation indicates that the 3D mouse from Connexion (Space navigator) is supported. I have just asked the company, but they didn't know anything about Chimera. I am wondering, whether you have some good experience using it, or whether you have an alternative mouse model that would work nicely together with Chimera. Tx -Thomas Here is the link at your documentation site: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#otherinput ------------------------------------------------------------------------------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

3 2

controling multiscale models from command script
by Marhoefer, R (Richard) 18 Jun '09

18 Jun '09

Dear Chimera Users, for the production of a movie file I like to control some attributes of a multiscale model e.g. the style and the surface transparency through a Chimera command file. Unfortunately I couldn't find many commands allowing to do so in the documentation. How could that be done? Kind regards, Richard Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

3 2

Minimize and solvate with a zinc ion
by Dr. Jean-Didier Maréchal 12 Jun '09

12 Jun '09

Dear all, I want to solvate then minimize (few steps) a structure with a zinc (Zn2+) ion. >From what I saw in the manual, zinc parameters are available in the actual version of the amber force field in chimera. However, I am stuck with troubles. When I solvate I have the following message: Could not determine charges for pre-existing solvent from added solvent for: Zn Zn What do I do wrong? All the best, JD *************************************************** Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

2 1

Chimera-users June 2009