[Chimera-users] Higher order

Tom Goddard goddard at cgl.ucsf.edu
Tue Jan 13 08:44:28 PST 2009

Hi Hernando,

  Multiscale models assigns colors by chain by default.  All copies of 
chain B will initially get the same color.  All copies of chain C get 
another color.  If you wish to change those colors, select a chain 
surface, click the select Copies button, then use the Color button or 
the Actions / Color menu (in Chimera 1.3 or newer).

  Maybe the case you are thinking of is where chains B and C are really 
copies of the same protein with different conformations.  If you select 
the surface for chain B you can then select all chains which have 
identical amino acid sequences with shortcut xc, then color those.  Now 
if you have several chains that are the same protein but have different 
sequences (maybe some residues not observed in some of the copies) then 
they are not identical.  Then you'd just have to hand-select one copy of 
each chains known to be the same, press the Copies button and color.  
This is the situation with rice dwarf virus 1uf2.  Might be nice to have 
the ability to extend selection to all chains that have the same chain 
name (given in PDB file though not currently used in Chimera).


hsosa at aecom.yu.edu wrote:
> Is it possible to assign colors by chain  to the surfaces created my the 
> multiscale models tool ?
> Thanks
> Hernando

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