On Jul 31, 2020, at 4:58 AM, Chin-Bow, Stephen stephen.chin-bow@yale.edu wrote:

Hi Elaine, I just searched for:

chimera 2D labels +gui

but I did not find it. Is it possible that the 2D Labels GUI was added for ChimeraX users? Many thanks! Stephen

Hi Stephen, Chimera's 2D Labels tool is in the menu under Tools... Utilities, and also under Tools... Depiction.

In general every command manual page also has a crossreference link to its tool, so you could just look at the "2dlabels" command manual page to find out about the tool. We generally just call the graphical interface dialogs "tools" so you wouldn't see the jargon "gui" very often in the documentation or find it in a search. If you just searched for "2d labels" you would find it. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html

The 2D Labels tool is also mentioned in the "tips on preparing images" and used in many of the image-making tutorials. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html

Another way to find out about the tool is to look at the Tools index in the User Guide. Each tool's individual manual page says what tool category it is in (which is the submenu under Tools in which it appears). http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html

ChimeraX does not have a 2D Labels GUI (tool dialog) yet, only a 2dlabels command. We changed the syntax of this command between the two programs, to simplify/improve it in ChimeraX.

Regarding your other message, we had envisioned new users finding out about Chimera features in these ways:

(1) tutorials: numerous in the User Guide and additional ones on our website (2) using menu Help... Search Documentation to search for terms of interest (3) browsing the User Guide (included with download, menu Help... User's Guidef), scanning through tools index, commands index, basic functions outline for topics of interest (e.g. "tips on preparing images") and then following the links to read more details. (4) website feature highlights, image gallery, and animation gallery

This does not address learning the programming (python) side of things. Chimera includes a Programmers Guide, but information for programmers is much less detailed than for users. http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html

ChimeraX has much more emphasis than Chimera on supporting programmers (APIs, programmer documentation, ...), as well as a Toolshed online repository for plugins (similar to the Cytoscape App store).

I hope this clarifies things. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco