Hi Brian, Documentation for the Chimera Multiscale Models tool that is described in that paper is in the Chimera User's Guide: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemul... The subsection on selecting components would be relevant. Here's a little tutorial on display of viruses using this tool. http://www.cgl.ucsf.edu/chimera/tutorials/virus-howto/showvirus.html In practice I would select the outer capsid of bluetongue virus (2btv) by selecting one chain with the mouse (ctrl-click on it) then use the keyboard shortcut that extends the selection to all chains with the same sequence (shortcut "xc" - extend to equiv chains). When the paper was written that didn't exist. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.... If I forgot about shortcut xc my next quickest route would be to select the two inner chains using ctrl-click, then shift-ctrl-click through holes in the outer capsid, then press the Copies button on the multiscale dialog then menu Select / Invert on the main window. If I really didn't know much about the capsid I'd probably select one chain of each different color in the outer layer (ctrl-click, then shift-ctrl-click to add more) then press the Copies button. All of this presumes you don't have any hierarchy info. The paper describes how with a script it is possible to define a hierarchy of structures (trimers, outer capsid, inner capsid, whole capsid). Unfortunately a script is still needed to do that. The script for that is in the above Chimera User Guide documentation under Structural Hierarchy. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/bluetong... You open the script file in Chimera (File / Open) to show the capsid with the hierarchy, then select one chain (ctrl-click), then press the Up button on the multiscale dialog to promote to the trimer, all trimers, .... That script had to work around an error in the 2btv PDB file which has since been fixed by the PDB. So the original script doesn't work unless the script is edited to remove "given = True". I've made that change in the online development documentation. Tom Brian and Lanie Grech wrote:

Hi everyone

In reference to the publication in the March 2005 edition of Structure, titled “Software extension to UCSF Chimera for interactive visualization of large molecular assemblies”. Under the subheading “Selecting subassemblies”, page 480, it talks about two methods to select part of the outer capsid layer of the model of bluetongue virus and not the inner capsid layers. I am unable to find the documentation explaining how to do this, could someone please direct me to the documentation or explain how to do this.

Regards

Brian Grech

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