[Chimera-users] Higher order

hsosa at aecom.yu.edu hsosa at aecom.yu.edu
Tue Jan 13 12:04:04 PST 2009

Thanks Tom, Now I can change the colors on each chain.
Another issue is that after displaying the surfaces of a big complex (33 
copies as BIOMT entries) chimera seems to freeze for very long periods 
of time.  It may be related to not having enough computer power (Dual 
Xeon 1.4 GHz,, 1GB RAM,  Windows XP,  Graphics ATI Radeon 9550, Chimera 
1.3) ?.


Tom Goddard wrote:
> 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).
>    Tom
> 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

Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone	(718) 430-3456
FAX	(718) 430-8819
email	hsosa at aecom.yu.edu

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