[chimerax-users] clickable commands

[Krishnan Raman]

Thank you so much.

-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, September 16, 2022 10:42 AM
To: Krishnan Raman <RKrishnan at BIOCRYST.com>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] clickable commands

[EXTERNAL]

Hi Krishnan,
You would write the HTML in a text editor of your choice.

>From my previous reply:
<https://link.edgepilot.com/s/54afaad7/-7jVZEtl4UOokEFYnyEc6A?u=https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-September/004315.html>

> ...Then in the HTML with special execution links, you could execute command "open blah.cxc" or even individual commands (or semicolon-conjoined small sets of commands).  This mechanism is explained here:
> <https://link.edgepilot.com/s/4a421f57/AQ-mNzU_kU2KyBbPC8OElw?u=https:
> //rbvi.ucsf.edu/chimerax/docs/user/tools/helpviewer.html>
>
> ....and the Quick Start Guide and some of the other tutorials exemplify this approach for individual/few commands per link:
> <https://link.edgepilot.com/s/885c4c67/rIa_Y6E1IEucZT4lxuoeZQ?u=https:
> //www.rbvi.ucsf.edu/chimerax/docs/quickstart/index.html>
> <https://link.edgepilot.com/s/12b9ee9a/CMBOGkl-L0_I0DLF3QfZUg?u=https:
> //www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html>
> ...etc...


See that first link above for how to encode execution links.  You can also "save source" of any of the tutorials with such links as examples of HTML with the special links.

You can also save the Log (which shows past commands one by one) as HTML with executable links, although I doubt that is what you want.  Your commands would probably instead be "open something.cxc" to execute a whole script, and you wouldn't want the other stuff that appears in the Log.  But anyway, how to do it:

(1) first use the Log context menu (right-click or Ctrl-click depending on type of computer) and choose "Executable Command Links"
<https://link.edgepilot.com/s/ee4317af/fgby6w8zQEiXaZQCAtAcfQ?u=https://rbvi.ucsf.edu/chimerax/docs/user/tools/log.html>
(2) use the Log context menu again and choose "Save As..."  (or use command "log save") <https://link.edgepilot.com/s/7d318ff6/3mZulRWE3U6R-NemgLvxlw?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html>

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

> On Sep 16, 2022, at 6:54 AM, Krishnan Raman via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> How  do I  make an html file for chimerax with clickable(executable) commands?
>
>
> Krishnan Raman
> Executive Director, Structural Biology BioCryst Pharmaceuticals
>
>
>
>
> CONFIDENTIALITY NOTICE
>
> This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.
>
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://link.edgepilot.com/s/01722bff/bAcPnC8K1U6xpHjy3f6Aaw?u=https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users



Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning.
CONFIDENTIALITY NOTICE

This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.