Eric Martz wrote:
Thanks very very much, Miguel, for making the choices so well organized and clear.
I vote for 3C (or 3B OK as second choice).
I vote for 1B, which would be the most flexible.
1 because you may easily use select commands before using color group to mimic the other effects 0, 2, 3.
B because if the PDB file is annotated 'wrong' concerning the chain, the PDB file is accessible by the user. With the other case it could not be manipulated, if there are missing residues (because of bad resolution) and Jmol detects a 'chain break' and 3C.
Regards, Jan
Among 1A, 2A, 3A, I prefer option 3A. Reasoning:
Option 1 is similar to RasMol/Chime (R/C) and is not very satisfactory.
Option 2 or 3 is how I wish R/C behaved.
Option 3 is more flexible -- it can generate an option 2 result if desired based on what is selected before coloring is applied.
Among A, B, C, I prefer C (B also OK).
However, it might be useful to have an option for 3A as well as 3B/C; the latter would be the default, but if you want to see if there are sequence numbering irregularities, 3A could be quite useful.
Reasoning for 3C:
Coloring by chain will make polymer vs. chain issues obvious, I think.
Therefore, we don't need an option to 'color group' by chain; 'color group' can always color polymers. (It's a little hard to be sure without having some experience with these exciting new capabilities.)
-Eric
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