ChimeraX : Cannot recommend to my class until minimization with vital cofactors such as FAD, NADH is built in. Returning to Chimera.
Dear Sir or Madam,
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
Novel Meritorious Research (and teaching) —•—•—•—•—•—•—•—•—•—•—•—•—•— A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/
Visiting Fellow, Einstein Foundation of Berlin
Dear Anne-Frances, I am sorry that your attempt to update your course to ChimeraX did not work out. When we implemented ChimeraX we focused on capabilities that were not in Chimera so that it would attract a user base of its own, at the cost of initially omitting some "meat and potatoes" capabilities that are nonetheless important to some types of everyday scientific analysis, as well as user interfaces to make some tasks easier. We recognize that these features are important and have been working on backfilling in these missing capabilities but, as you discovered, that process isn't complete. The porting process is more time consuming than you might think because of the differences between Python 2 and 3, between the design architecture of Chimera and ChimeraX, and because some third-party libraries were never ported to Python 3 (e.g. MMTK, used for minimization). If you like, I could add you to the recipient list for the enhancement-request tickets we have open for the capabilities in our bug-tracking database, so you can keep tabs on when these features get implemented. Though we are not actively developing Chimera, we are attempting to keep it working as best we can given our funding and resources. The one thing you mention that really is already done is the transparent-background thing. As Tony Schaefer mentioned, you can abbreviate the option to something like "trans t", and if you use the File→Save dialog there is a "transparent background" check button for image formats.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 9, 2024, at 3:55 AM, Anne-Frances Miller via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Sir or Madam,
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
Novel Meritorious Research (and teaching) —•—•—•—•—•—•—•—•—•—•—•—•—•— A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/
Visiting Fellow, Einstein Foundation of Berlin
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participants (2)
-
Anne-Frances Miller -
Eric Pettersen