- Chimera-users - RBVI Mailing Lists

[Chimera-users] chimera-1.1917-linux.exe: Exec format error. Wrong Architecture.
by Pattanayek, Sabuj 12 Mar '04

12 Mar '04

I'm getting this error when I try to run the installation -rwx------ 1 root root 26226504 Mar 12 12:02 chimera-1.1917-linux.exe [root@eglimp]# chimera-1.1917-linux.exe chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. [root@eglimp]# ./chimera-1.1917-linux.exe ./chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. [root@eglimp]# md5sum chimera-1.1917-linux.exe 67e955ce87d000916039d94c7d6d0a56 chimera-1.1917-linux.exe [root@eglimp]# uname -rs Linux 2.4.22-openmosix2smp web page: linux chimera-1.1917-linux.exe Size: 26226504 bytes MD5: 67e955ce87d000916039d94c7d6d0a56 Thanks in advance Sabuj Pattanayek

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mac version of 1.1917 snapshot
by Eric Pettersen 10 Mar '04

10 Mar '04

Hi again, If you downloaded the Mac version of 1.1917 before about 5pm PST today, you should download it again because we updated it to fix a bug. The non-Mac versions are fine. The Mac version was not displaying atoms in stick, ball-and-stick, or sphere modes (wireframe mode was okay). Sorry for the possible inconvenience! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu

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new snapshot release (1.1917)
by Eric Pettersen 09 Mar '04

09 Mar '04

Hi, We've just put a new snapshot release of Chimera up for download on the web site (http://www.cgl.ucsf.edu/chimera) Here are the highlights of the changes between this snapshot (1.1917) and the previous one (1.1892): tools: Match -> Align can create sequence alignments for multiple matched structures (not just pairs) Multalign Viewer can show/edit sequence annotations for relevant formats (RSF, Stockholm) SimpleSession -- saves label font/size and secondary structure assignments -- compiles to .pyc file: 50% less memory use, 15% less time to restore added Export Surfaces as VRML (in Utilities category) -- save surfaces made by Multiscale Models and Volume Viewer as VRML files added Browser Configuration (also in Utilities) -- configure browsers to send certain file types to Chimera (see also new Web Data preferences) FindHBond and PBReader allow line width to be set Movie has preliminary support for reading GROMOS trajectories newly available commands: bondcolor -- color bonds independent of flanking atoms bonddisplay -- set how bond display depends on flanking atom display bondrepr -- set bond representation to be wire or stick (independent of atoms) hbonds -- command equivalent of FindHBond tool rlabel -- whether residue name/number is included in the first atom label per residue Model Panel new 'render attrs...' button allows coloring by model/residue/atom attributes (e.g. B-factor) The 'render attrs...' interface is in preliminary form and will be changing. It also isn't documented yet but is pretty easy to use. Just pick an attribute of interest and a histogram of values will be displayed. By default there will be three color bars on the histogram that you can grab and move around with the mouse, or add or remove with control-click. You can use the 'Color' color well to set the color of the last bar you picked. The 'No value' color well is used in the rare case of the attribute being missing (or set to None) in the atom/residue/model. Click Apply or OK to make the coloring happen. Several parts of the interface are grayed out since they haven't been implemented yet. In the future you will be able to select by attribute value, and change atom radii or ribbon widths based on attribute values. If you are using the last production release (1.1872) instead of the previous snapshot, then you will also be getting these features when you go to 1.1917: general: additional file formats for saved images (PS, EPS) different lighting scheme in graphics window (over-the-shoulder instead of headlight) tools: added Shininess Control (in Viewing Parameters) -- adjust shininess, brightness, and the color used for shiny highlights Collaboratory section in Preferences allows designation of port number and IP address (for firewalls/NAT) Movie -- allows definition of scripts to be run at each time step -- looping can be turned off Multalign Viewer allows structure selection by arbitrary % residue conservation Volume Viewer options added to subdivide and smooth isosurfaces commands: copy command now offers supersampling and PS/EPS formats new ribbackbone command controls whether ribbon and backbone atoms are shown simultaneously Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Use of Chimera for Trends Plant Sci March 2004...
by John F. Allen 24 Feb '04

24 Feb '04

....for article and issue cover illustration. Final proofs attached. Acknowledged. Great program. Will send reprint(s) and final pdf on request. Many thanks John F. Allen Professor of Plant Cell Biology Plant Biochemistry Center for Chemistry and Chemical Engineering Lund University Box 124 SE-221 00 Lund Sweden Tel: +46 46 222 7788 (Office); +46 46 222 4073 (Laboratory) Fax: +46 46 222 4009 (Direct); +46 46 222 4116 (Departmental) E-mail: john.allen(a)plantbio.lu.se Plant Cell Biology: http://plantcell.lu.se Publications: http://plantcell.lu.se:591/john/

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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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