Sorry I sent the first version from a personal address. Please respond to this one :-) Novel Meritorious Research (and teaching) —•—•—•—•—•—•—•—•—•—•—•—•—•— A.-F. Miller, Ph. D. (she/elle/sie) Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/ Visiting Fellow, Einstein Foundation of Berlin
On Jan 12, 2025, at 16:49, Anne-Frances Miller <afmill3r@gmail.com> wrote:
Hello Elaine,
You are right there are some very nice improvements that unite related but idiosyncratic commands, such as surfrep. Thank you !!
Unfortunately many obsolete are still in your getting started tutorial https://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html This tutorial needs a LOT of corrections so I attach a pdf in which I have done that, for all the commands (page 13 and later). The menus are less problematic. Please see the magenta text I've added and the text with strike-throughs (not obvious, you'll have to look).
Because it might be easier, I also provide my 'tips' (corrections) that I included in the course handout.
If there is a person in charge of the tutorials, please give the attached to them and please put me in touch with them, since I wanted to use some of the others but now am afraid to do so. It would be great to know when each one was updated, and for what version of ChimeraX.
<Getting Started with UCSF Chimera.pdf>
TIPs: When you want to open a file that resides on your computer, File>Open... or command: Open browse.
To specify a chain, use /B or /b before the residue name instead of .B or .b after it. Use /B :Lys instead of :Lys.B.
All commands use the sequence command <specify atoms to apply it to> keywords <target representation>. E.g.. color :Lys green byhet or color /a tan cartoon. (the ‘cartoon’ is the ribbon diagram for a protein, ‘ribbon’ can be used instead Col ligand fromatoms surface would apply the coloring each of the ligands’ atoms has to their associated surfaces.
You can pull the various secondary GUIs off the graphics window to put them in more convenient places on your screen.
The ‘Favorites’ menu no longer exists, see ‘Tools’ for most of its contents. For example to open the side view: Tools>General>Side View.
When you select something, via the mouse or via select. The number of atoms, residues, and models selected will be reported beneath the command line. This is exceedingly useful information as it informs you whether you got want you want.
To see all the named colours via menus use actions>color>all options then click ‘Show all colors’ in lower right. Command: color list provides all of them in the log.
Color <specify what you want to color> byhet (applies CPK coloring, leaves C alone).
For any command giving you trouble, type command: Help <the command>. For example, for help on the color command type help color. (Well worth it!)
The old command ‘represent’ no longer exists, use style. E.g. style :Cys sphere.
The old command ‘surfrep’ also no longer exists. Use surface style. E.g. surface style #1.2 solid . #1.2 means the second surface in model #1. For example if there are different chains/subunits in model 1 /a will yield surface 1.1 and /b will yield surface 1.2)
Transparency can be applied to an atom specification (e.g. your choice of residues), and a particular representation (e.g. the surface or the ribbons). Transp /b 50 surface makes the surface of subunit B 50% transparent.
To save your work, use the menu item file>save... and choose as file type a ChimeraX session or just give your file the .cxs extension. The toolbar also has a save option, but it seems to save to my desktop regardless of my chosen working folder (chosen via the menu File>Set Working Folder). Weirdly, I did not find the save as well as the save as options, so you have to explicitly overwrite your earlier saves.
- • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836
https://millerlablive.wordpress.com/
Visiting Fellow, Einstein Foundation of Berlin
On Jan 10, 2024, at 17:23, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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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