Hi Warren, I think both plans for default values of smooth_loops and ribbon sampling are good ones. This reminds me of a question I had yesterday while working in PyMOL 0.93 -- if I want to use ribbon_sampling values unequal to 1, should I downgrade to an earlier PyMOL (e.g., 0.92)??
Thanks for any advice, Cameron > PyMOL Users: > > 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 > default) > > 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 > above proposals. > > Cheers, > Warren
