[Chimera-users] Using Select with multiscale models

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 24 08:57:09 PST 2013


Hi Peter,
Multiscale Models creates the copies as low-resolution surfaces, without loading the full atomic coordinates (for computational efficiency).  It will then load additional copies of the full atomic coordinates only as needed, e.g. when you choose to show a chain in any of the non-surface styles.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>

The command-line specifications mostly refer to atoms, which are not present in the low-res-surface copies.

Probably the "msc" command is what you need.  First you would color the atoms in the original copy of the structure, and then "msc" will color the low-res surface of that copy to match the atoms, and is also smart enough to propagate the same coloring to the other copies' surfaces even though their atoms haven't been loaded.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msc.html>

That approach avoids loading the atoms. The other approach is to actually load all the atoms (use the Multiscale Models dialog to select all chains and show them in any non-surface style, e.g. ribbon... that would load models #2, 3, ...), color the atoms of all the copies as desired, and then use Color Zone (under Tools... Volume Data) to color the low-res surfaces to match the atoms. However, that may be too many atoms for your system to handle conveniently.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 23, 2013, at 10:11 PM, <Peter.Durr at csiro.au> wrote:

> Hi
>  
> I am using Chimera to try to visualise and then highlight the position of several amino acid mutations on a virus capsid.
>  
> I have managed to use the Multiscale module to build the capsid from a PDB file.
>  
> My next step is to select the residues of interest.
>  
> I am able to use the Select command to find the residue within the icosahedral asymmetric unit – e.g. “select #0:14.A”
>  
> However, when I apply the same command  to the modelled surfaces, it doesn’t work.
>  
> More specifically when I run “select #1:14.A” at the command line – nothing happens - not even an error message.
>  
> However, I can hunt around in the modelled surfaces  on the screen and then use the mouse to interactively select the residue of interest – so Chimera seems to know which residues are which on the modelled surfaces.
>  
> Thanks in advance for any guidance on how to deal with this problem.
>  
> Peter Durr




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