[Chimera-users] Molecule fusing

Tom Goddard goddard at sonic.net
Fri Oct 15 16:02:14 PDT 2010

  Hi Brian,

   Yes, if you want to make a density map for a VP7 trimer of rotavirus 
and you had 3 monomer VP7 atomic models opened and positioned to make a 
trimer in Chimera you would make the map with Chimera command:

     molmap #0-2 8

where the monomer model numbers are 0, 1, 2 in this example and the 
desired map resolution is 8 Angstroms.  As Elaine pointed out, if you 
want to make an entire virus capsid map calculated from atomic models 
you may run into trouble because Chimera will take too much memory for 
the millions of atoms.  Still it may be possible, but I would reduce the 
atomic models to C-alpha atoms only.


> Hi Sir/Madam
> I want to create models which consist of multiple protein molecules, 
> in which the individual protein molecules are fused together to form a 
> single structure. Something like the scanning 3D maps produced by 
> electron microscopes. Is it possible to do this with the Muliscale 
> Models tool or some other tool or method in Chimera?
> An example of what I want to do appears in the cutaway rotavirus 
> illustration (Fig. 1A) in Chen and colleagues paper, titled, 
> "Molecular interactions in rotavirus assembly and uncoating seen by 
> high-resolution cryo-EM" (PNAS, vol. 106. no. 26, p. 10644). In this 
> illustration the yellow triangular shaped structure are multiple VP7 
> molecules fused together.
> Regards
> Brian Grech

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