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 -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
