[Chimera-users] how were the virus images generated?

Thomas Goddard goddard at cgl.ucsf.edu
Tue Apr 5 10:55:16 PDT 2005

Hi Dieter,

  To make virus capsid images in Chimera like those on the VIPERdb web site,


or like those on our web site



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.


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,


> From: "Dieter Blaas"
> To: goddard at 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, 
> ------------------------------------------------------------------------

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