[Chimera-users] Can I use wait command over Rest service?

Mungo Carstairs (Staff) g.m.carstairs at dundee.ac.uk
Mon May 30 10:46:27 PDT 2016

Hi Elaine,

Thanks. I tried as separate commands and now at least I can see the effect, but only as a fast flicker regardless of the wait value (or no wait command).
It does seem that wait is ignored over Rest. I guess I could code the wait at my end but that would be a last resort.

Concatenating the commands on the command line does give the wait behaviour I am hoping for (so somewhat contradicts the link you passed in that the display is redrawn a couple of times).

Sleep works, but is too slow for my purposes (minimum one second delay), which include tracking over a sequence with the mouse at some speed.


Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.

From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 30 May 2016 18:26:11
To: Mungo Carstairs (Staff)
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Can I use wait command over Rest service?

Hi Mungo,
If I understand correctly, stringing the commands together with semicolons means to only show the result at the end.

“...display is not redrawn until the last command in a semicolon-separated series has been executed.”

 I’d expect it to behave more like you want as two separate commands:

display #0:30.A;wait 20
~display #0:30.A

… although perhaps that is more trouble to script.  If this is just for “live” execution (not recording as a movie) the “sleep” command may be an alternative to “wait,” although it may also require using two separate commands.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 30, 2016, at 9:58 AM, Mungo Carstairs (Staff) <g.m.carstairs at dundee.ac.uk> wrote:

> Hi,
> I am trying to devise a way to highlight locations on a structure in Chimera while mousing over the sequence in Jalview.
> My latest attempt tries to 'flash' the side-chain display at the residue position i.e.
> - hide then show atoms (if currently displayed e.g. display is in atom mode)
> - or show then hide atoms (if currently not displayed e.g. display is in ribbon mode)
> I'm sending a command like
> display #0:30.A;wait 20;~display #0:30.A
> to the Rest service.
> However while this seems to do what I want when used at the Chimera command line, via the Rest service it ignores the wait command, with the result that the action is too quick to see.
> Any suggestions please for how to get this to work, or a better alternative?
> Thanks,
> Mungo

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