After devoting several days to updating three weeks of my course to use ChimeraX instead of Chimera, I am returning to Chimera.

ChimeraX may be a great cutting-edge tool, but it is not ready for a wider audience until it can make ‘common’ tasks easy. Please do not distance research from science. We desperately need science to be exciting and accessible to a wide audience. Chimera does that. ChimeraX does the opposite, sending the clear message that only an elite few are deemed worthy. Please please please, open the door to wider use, for the sake of science, and for the sake of the citizens of our country (who fund your agencies via taxes). 

Very Helpful - To make images with transparent backgrounds, members of my class as not going to type out ’transparentbackground true’ (even my emailer wants to spell the first string as two words).

CRUCIAL - in-program minimization that includes critical cofactors (present in >40% of all enzymes and the actual source of their activities often!!) FAD, FMN, NAD(H), how is this anything more than structural biology if the sources of activity are not included? (‘biology’ implies life. Life REQUIRES chemical reactivity.)

CRUCIAL - in-program trajectory analysis that can tabulate (for example) a distance, frame-by-frame and allow export in tabular form.

Very Helpful - worms with thicknesses that can represent an attribute. These provide a critical orthogonal way to add a second attribute when color is already in use for a first.

Very Helpful - Lighting/effects/side view GUI that allows easy optimization of figure reflectivity, special effects, all in one place and does not require users to remember what Cartesian coordinates they gave their first light. It is so much faster and delivers much better results than ChimeraX.

This email records the current worst applicability gaps only, I see others have reported more. 

I would like to like ChimeraX, but as a person trying to bring science to wide audiences, ChimeraX is the best argument for Pymol I have seen in a while. Do not stop supporting Chimera until ChimeraX can serve real humans, please!

Sincerely, 

and thanks to the team,

Anne-Frances