Re: [Jmol-users] coloring peptide chains

[William R. <whr...@ms...>]

Miguel,
I was hasty in posting my question, because within the hour I 
rediscovered how I had done this in Chime, and it works fine in Jmol.
My script syntax is:  select protein;  select *A; color atoms blue;  
select *B; color atoms red; (or whatever colors you wish).
However, I now have a different problem. I wanted to use this technique 
in showing the different segments of hemoglobin, but the pdb file for 
this compound appears to be too large for Jmol to handle. It loads in 
Chime, but does not display in Jmol. Is there a size limit on the 
structures Jmol will handle?
I had noted earlier that the very large protein ricin failed to load as 
well.
Bill

Miguel wrote:

>Bill wrote:
>  
>
>>When displaying structures composed of two or more peptide chains, e.g.
>>insulin, the chains may be given different colors by the color chain
>>command. In both Chime and Jmol the colors are designated by default. Is
>>it possible to assign other colors to the chains? I have not found a
>>Rasmol command that permits this to be done.
>>    
>>
>
>There is no direct way to assign different colors to the chains ... but
>there is a workaround.
>
>Jmol uses different colors and a different algorithm from RasMol/Chime.
>
>RasMol/Chime starts with the same color, regardless of what the chain
>identifier is.
>
>Jmol always uses the same color for the same chain identifier. And the
>Jmol colors are shades of pastels.
>
>The workaround is as follows:
>
>You can select sets of atoms and color them however you want. So you can say
>
>select :a; color atoms salmon
>select :b; color atoms orchid
>select :c; color atoms lightSkyBlue
>
>Take these script commands and put them in a file called
>´myChainColors.txt´. You can then say
>
>script myChainColors.txt
>
>Whenever you want to apply these colors.
>
>
>Miguel
>
>
>
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