Re: [Jmol-developers] Changing cpk colors

[Rolf H. <rh...@im...>]

Miguel wrote:
> Rolf wrote:
>>>(Jan, I believe that you asked for this a *long* time ago)
>>>
>>As Jan's successor at the FLI Jena (former IMB Jena) I know why he asked
>>for this. It will help to simplify scripting at the "Jena Image Library
>>of Biological macromolecules".
> 
> I did not know that Jan was gone ... send him my best wishes.
> 
>>Q: Could you extend this possibility to change the default colors  of
>>secondary structure elements?
> 
> I will see how difficult it is.
> 
> Q: Why do you want to change the colors?

This was not my decision. I quess it was decided several years ago by 
Jan and his (and now my) chief. I just have to adjust the scripts for 
the Jmol user interface I am currently developing for the FLI.

But I can guess why they changed the colors for secondary structure 
elements. At the "Jena Image Library of Biological macromolecules" the 
images are usually created with a white background. Since 'white' is 
used for 'other' (appearing quite often in structures from the Protein 
Data Bank) they could not really stick to the default colors.
Printing is another problem. If you try to print yellow (used for 
beta-sheets) in greyscale the result is not very impressive.
Besides I must admit that I prefer their colors (red for alpha helices 
and blue for beta-sheets), even on a black background.

> 
> Q: Don't you think it is best that everyone use the same colors?
> 
> 

In principle I would agree. But if the default colors weren't selected 
very well and if there are good reasons for a change, I wouldn't stick 
to the default colors for any price.

Regards,
Rolf