Regarding default setting:.
1) How many people will object if I change PyMOL's default cartoon settings
so that loops are not initially smoothed? (cartoon_smooth_loop = off by
The reasoning behind this is that gross smoothing is really only appropriate
for publication-quality illustration of large structures, but increasingly
people are using PyMOL as a tool for visualizing & animating molecular
structures and interactions in real time.
Having smooth_loops on as a default means that the cartoons are not
representative of the true backbone coordinates, which is a source of
confusion for some and consternation for others.
This change will affect existing scripts, but not session files. All you
would need to do is add "set cartoon_smooth_loops = on" to your script in
order to recover the prior behavior.
2) How many people will object if I change PyMOL's default ribbon sampling
to 1 -- so that by default ribbon is essentially a C-alpha trace. Due to a
bug in 0.93, this was a locked seting anyway, so any recent scripts probably
already make this assumption.
Here is the reasoning is different: Ribbon is often used for getting a
simplified idea of the overall protein fold, and to identify regions of
interest. Only with ribbon sampling = 1 can you identify the location of
the CA position on the ribbon. Otherwise it visually ambiguous unless you
have other representations visible.
By the way, use of ribbon under cartoons to have a "pickable" representation
is no longer necessary since Cartoons are now "pickable" using the mouse.
Please let me know if you have a strong opinion regarding either of the
Warren L. DeLano, Ph.D.
DeLano Scientific LLC