- Chimera-users - RBVI Mailing Lists

get to lighting adjustment
by jinghua＠ucsd.edu 26 Apr '05

26 Apr '05

to whom it may concern, How could I get to the adcanced feature of lighting adjustment? Can I add more lights with different directions? Thanks! Jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>< Jinghua Tang, Ph.D. Phone: 858-534-5852(o) 4107 Natural Sciences Bldg, MC-0378 858-597-2056(h) Department of Chemistry & Biochemistry Fax: 858-534-5846 University of California, San Diego E-mail: jinghua(a)ucsd.edu La Jolla, CA 92093-0378 http://jinghua.ucsd.edu <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><

2 1

Writing the selection
by Charles Moad 19 Apr '05

19 Apr '05

How can I write the current selection to a file from a script? "write sel filename.pdb" does not work. Thanks, Charlie

2 2

v1.2105 for amd64 (x86_64)
by Sabuj Pattanayek 18 Apr '05

18 Apr '05

Hi, I don't know if this has been asked before (couldn't find anything on searches) but will there be a native amd64/emt64 (x86_64) build of chimera v1.2105? Thanks, Sabuj Pattanayek

2 1

Problem with Large Molecules
by Private 14 Apr '05

14 Apr '05

Dear Chimera Team: I think your work on Chimera has been of very high quality. In fact, I've used it to produce print quality images for an upcoming book of mine. However, I've had some problems with displaying some large molecules, for example, 1AYM and 1P5Y. I use the PDB file for the molecule, but specifically the assumed biological model file, not the the asymmetric unit file. I've been able to open the file in programs like Deepview and Raswin, but I can't open the file in Chimera. I'm running Windows 98 with about 256MB of RAM, and what happens when I attempt to open the assumed biological model file Chimera runs for over an hour trying to open the file and then crashes with a page fault message. I certainly would like to use the image capabilities provided by Chimera, so can you help me with this? Or is this simply a limitation of Chimera?

2 3

Thanks for the movie recorder
by Ann Mullin 08 Apr '05

08 Apr '05

I just tried out the movie recorder and I am very pleased. Thanks very much to the programmers who contributed to the addition of this tool to my favorite molecular graphics program. Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amullin(a)tulane.edu

1 0

yet another snapshot
by Eric Pettersen 05 Apr '05

05 Apr '05

A new snapshot release (1.2106) is available for Windows only, which fixes several issues the 1.2105 release had on that platform, namely: Movie Recorder movie encoding now works documentation searching fixed unreadable highlighted text in certain widgets fixed Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

how were the virus images generated?
by Thomas Goddard 05 Apr '05

05 Apr '05

Hi Dieter, To make virus capsid images in Chimera like those on the VIPERdb web site, http://viperdb.scripps.edu/ or like those on our web site http://www.cgl.ucsf.edu/Research/virus/ http://www.cgl.ucsf.edu/chimera/ImageGallery/ you use the Chimera Multiscale tool, menu entry Tools / Multiscale / Multiscale Models. I'm guessing you tried making solvent excluded molecular surfaces with menu entry Actions / Surface / Show. That makes much higher resolution surfaces and tends to crash for large molecules or complexes. (We are working on replacing that third party code.) If your virus capsid PDB file header contains sixty REMARK 350 BIOMT matrices then you can just press the "Make Models" button at the bottom of the Multiscale dialog. This uses the matrices to make sixty copies of the asymmetric unit. You don't need a file containing coordinates for the full capsid with this tool. If your virus capsid PDB doesn't have the BIOMT matrices, but uses the coordinate system defined by the VIPER site (eg a PDB downloaded from VIPER), then you can instead choose Multimer Type: Icosahedral Symmetry, VIPER Z(2)35X(2) from the menu at the bottom of the Multiscale dialog, and then press the "Make Models" button. Once you have displayed the capsid model, you can color, hide, or display capsomeres at atomic resolution or with ribbons using the other buttons in the Multiscale dialog. For the full details look at the Tools section of the Chimera User's guide for Multiscale. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… You can show this documentation in a web browser by just pressing the Help button at the bottom of the Multiscale dialog. Let me know if you have additional questions, Tom > From: "Dieter Blaas" > To: goddard(a)cgl.ucsf.edu > Date: Tue, 05 Apr 2005 12:38:20 +0200 > Subject: how were the virus images generated? > > Dear Tom, > Vijay referred my question to you: As far as I > understand were the virus images in VIPER generated > with Chimera. I have tried hard to generate similar > surface renderings with this software on a win2k 2 GB > machine but Chimera always crashes upon trying to > make the surface! Are there any particular parameters > which must be set? What is the limit of atoms, > coordinates, surface resolution, RAM? Many thanks for > any hints. > > Regards, Dieter Blaas > ------------------------------------------------------------------------ > Dieter Blaas, > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > ------------------------------------------------------------------------ >

1 0

HAVING TROUBLE W/ PROGRAM!
by Desmond McMahon 05 Apr '05

05 Apr '05

I downloaded Chimera and I tried to understand the help section. I'm a high school student and i'm using this for a report. CAN YOU PLEASE PLEASE PLEASE tell me how to START a DNA/Double helix structure and I can't find out. Can you help me??? Desmond __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

2 1

by Andreas Linden 31 Mar '05

31 Mar '05

Hi, maybe you can incorporate drag and drop into chimera? It's a bit of a hassle having to go through file>open> and then go through directories to get at the pdb file! Otherwise an excellent program, thanks for making it available! Cheers Andy (University of Sheffield, UK)

2 1

new snapshot
by Eric Pettersen 29 Mar '05

29 Mar '05

We've put out a new snapshot (version 1.2105) which is basically the same as the 1.2104 snapshot but has the zone-selection crash bug fixed. --Eric

1 0