Hi Anne-Frances, yes I'm still here, and kind of you to mention me! We do feel the pressure to add those missing features, and many of them are listed in our "ChimeraX vs. Chimera" page: <https://www.rbvi.ucsf.edu/chimerax/progress.html> Just wanted to mention we've also tried to take "lessons learned" from Chimera to make ChimeraX easier to learn and use, such as: (A) Toolbar icons to perform many actions with a single click: hide/show surfaces, atoms, ribbons; change between commonly used lighting styles, hide/show silhouette edges, calculate H-bonds, show Side View, etc. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html> (B) Actions performed with these icons, with GUI tools, or the menu are shown as the equivalent commands in the Log, to make it easier to learn the commands (C) Making commands simpler and more mnemonic, e.g. - "close" closes everything - "save" saves most formats, instead of Chimera's separate "copy" "save" and "write" commands for different formats - using "/" for chains instead of the confusing "." that had to appear right after the residue numbers in Chimera - easier specification of two sets of atoms in the hbonds and contacts commands - vastly simplified morph command [etc.] Best wishes for a healthy and happy 2024, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 10, 2024, at 2:06 PM, Anne-Frances Miller via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you Eric, Tony, and Greg, and all the kind people who have already answered me. I regret that as I develop new modules for my course (using your golden-oldie Chimera), my response time has increased by x20. However I am very grateful that -1- I still see recent updates occurring to Chimera and -2- that you have taken the time to explain the strategy you are guided by, which indeed makes considerable sense.
I will (over the weekend) answer your individual emails, but I apologize for being much slower than you. If Elaine Meng is still with you, she set a high bar for support, and you appear to be keeing it up!
Anne-Frances
P.S.
- • - • - • - • - • - • - • - • - 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
On Jan 10, 2024, at 15:15, Greg Couch <gregc@cgl.ucsf.edu> wrote:
Just want to note that you should always use the untruncated versions of the commands in any command script. That way the scripts won't break in newer versions of ChimeraX when new commands or keywords are added.
-- Greg
On 1/8/2024 10:33 PM, Tony Schaefer via ChimeraX-users wrote:
Anne-Frances,
ChimeraX commands and their keywords can already be abbreviated, as long as enough of the word is typed for ChimeraX to identify the command/argument. For example, I can run `sa test.png t f` and ChimeraX expands this to `save test.png transparentBackground false`. This works because `save` is the only command that starts with "sa", `transparentBackground` is the only keyword it's expecting that starts with "t", and `false` is the only option it's expecting for `transparentBackground` that starts with "f".
See the Truncation section of this page for more details: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#...
Best,
Tony
On Mon, Jan 8, 2024 at 10:37 PM Anne-Frances Miller via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear Sir or Madam, Re. ChimeraX 1.7: the image save option ’transparent background true’ is very long, and typo-prone. Is there an abbreviation or short form please?
Thank you - • - • - • - • - • - • - • - • - 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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