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/framemul... 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@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, ------------------------------------------------------------------------