- Chimera-users - RBVI Mailing Lists

CHIMERA help - coloring density maps
by Padmaja Natarajan 02 Feb '04

02 Feb '04

Hi, I have just started using CHIMERA to look at volume files in the CCP4 format for virus particles. I would like to color the density as a color ramp continuously changing between ANY two specified colors depending on the radial distance from the center of the virus particle (as shown in the attached figure). How do I achieve this with CHIMERA? thank you very much for your help in advance. -Padma

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Chimera dead after NVidia driver install...
by Patrick Ladam 12 Jan '04

12 Jan '04

Hi all, I had chimera 1.1872 working OK on my MDK 9.2 Linux box until I installed the NVidia driver for my GeFOrce2 card. What happens now is that chimera launches but stops during start-up with an error box indicating this message: "Togl: Couldn't get visual" This sounds like an OpenGL problem to me but I am far from being a specialist on this. Does anyone have a clue how I can debug/fix this ? Bye -- ----------------------------------------------------------------- | Patrick LADAM | | | Laboratoire CSSB | THE BIG BANG THEORY: | | UFR SMBH | | | 74 rue Marcel Cachin | In the begining there was | | 93017 Bobigny CEDEX | nothing at all. | | e-mail: | | | ladam(a)smbh.smbh.univ-paris13.fr | Then, it exploded... | | Tel: 01 48 38 77 26 / 76 85 | | | Fax: 01 48 38 77 77 | | -----------------------------------------------------------------

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hi
by amutha ramaswamy 08 Jan '04

08 Jan '04

Dear Sir It is possible to make movies with PDB structurers in chimera. this would really be helpfull in visualing the conformatinal changes. I know chimera has the option for movie with trajectory files. but i wish to kow the option with PDB files only. Looking forward for your kind reply Sincerely Amutha Dr Amutha Ramaswamy Postdoctoral Fellow, Department of Biomedical Informatics 3184 Graves Hall, 333 West 10th Avenue The Ohio state University, Columbus, OHIO 43210 Phone: 614-688-3236 (Office); 614-291-0071(Residence) Fax: 614-292-7659 (Office) --------------------------------- Do you Yahoo!? Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes

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Re: save selected atoms in a pdb file?
by Elaine Meng 08 Jan '04

08 Jan '04

Hi Sabuj, You can make surfaces that surround a set of atoms without making a separate PDB file. For example, if you have those atoms selected already, just use the command: surfcat mygroup sel where "mygroup" could be whatever you choose to name this set of atoms and "sel" means what is currently selected. Then, the command surface mygroup will show surface surrounding that group. There are several ways you could select the atoms of interest, and it sounds like you already figured out that part; the following detailed example is just one possibility: open pdb:2gbp sel :glc z<4.5 ~sel :glc ~sel solvent surfcat nearby sel ~sel surf nearby Here I opened a glucose-binding protein structure, selected all residues with any atom within 4.5 A of the ligand glucose (glc), then subtracted glucose itself and waters from the selection. Then I made the selected atoms a surface category with "surfcat," unselected them, and showed the corresponding surface. If you really want to save the selection to a file, it can be done on unix systems. Chimera can send information on what atoms are displayed to the system, and then the system command "cat" can send the information to a file. In Chimera, if the atoms of interest are selected: show sel pdbrun nouser cat > ~homedir/myfile.pdb (where "homedir" is your username) saves the displayed atoms to a PDB file named myfile.pdb in your home directory. It is necessary to use show (which undisplays everything else) since pdbrun includes all atoms that are displayed. The coordinates are transformed, so will be different from the original coordinates if you have moved the view around. If you want the untransformed coords, use the "reset" command before the "pdbrun" command. This process doesn't work on Windows as there is no cat command. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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save selected atoms in a pdb file?
by Pattanayek, Sabuj 08 Jan '04

08 Jan '04

Hi, Is it possible to save only the currently selected set of atoms/bonds or the atoms/bonds currently shown in the display into a pdb file? This is would be useful when doing surfaces for a particular location (e.g. atoms surrounding a central cavity), since the command "surface selected" seems to leave gaps in inaccessible areas (behind the atoms surrounding the cavity). Thanks, Sabuj Pattanayek

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[Chimera-users] shininess/brightness/specular color of surfnet surfaces
by Pattanayek, Sabuj 05 Jan '04

05 Jan '04

Hi, Is it possible to alter the shininess/brightness/specular color of Surfnet surfaces? Also is it possible to save the surfaces so they don't have to be recreated every time? Thanks, ----------------------------------------------------------------- Sabuj Pattanayek Martin Egli Lab Vanderbilt University Dept. Biochemistry http://linegli.mc.vanderbilt.edu

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Old version for Sparky
by laurent volpon 05 Jan '04

05 Jan '04

Hello, I would like to download an old version of Chimera (1.1442) because I have to use it with the same Python version (2.1) as Sparky. I tried at http://www.cgl.ucsf.edu/chimera/distrib/oldreleases.html but I had this: "Error: The URL you used is malformed". Please can you help me to find this version, or is there a way to use the version I have (1.1872) with the version 2.1 of Python (instead of 2.2). Thank you by advance for your answer. Sincerely Dr Laurent VOLPON ______________________________ Dr Laurent Volpon 3575 Avenue du Parc, Suite 5315 P.O. Box #85 Montréal, Qc, H2X 4A3 tel.: (514) 847-9494 ______________________________ --------------------------------- Lèche-vitrine ou lèche-écran ? Yahoo! Magasinage.

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vdw viewer
by Terry Downing 23 Dec '03

23 Dec '03

Hey CGL, I would like to be able to visualize several different vdw parameter sets on the same molecule. Is there a way to visualize just the vdw surface? Can I change the parameter files easily? As always, thanks in advance for your help. Sincerely, Terry Downing -- P. Therese Downing Chemistry and Chemical Biology Graduate Program Kuntz and James Labs, UCSF Voice: (415)476-3986 Fax: (415)502-1411

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ribbon+atoms
by Eric Pettersen 22 Dec '03

22 Dec '03

Hi, the 1892 snapshot release we just put out allows control over whether backbone atoms can be displayed with ribbons (on a per-model basis). There is a "ribbackbone" command, an entry in the New Molecules preference category, and a control in the attributes panel (reached via the "attributes..." button in the model panel). Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu

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interactive volume segmentation
by Juha Huiskonen 18 Dec '03

18 Dec '03

Hello, currently it is possible to select only box-shaped subregions in Volume Viewer. I would be especially interested in segmenting electron density maps or their isosurfaces to different subregions with any shape interactively. Is anyone planning to add a feature like this? Regards, Juha Huiskonen

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