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

Elaine Meng meng at cgl.ucsf.edu
Mon May 30 11:19:05 PDT 2016


Hi Mungo,
At least in my tests, it is possible to use fractional sleep times, e.g. “sleep .1”
Best,
Elaine

On May 30, 2016, at 10:46 AM, Mungo Carstairs (Staff) <g.m.carstairs at dundee.ac.uk> wrote:

> 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
> 
> Mungo Carstairs
> Jalview Computational Scientist
> The Barton Group
> Division of Computational Biology
> School of Life Sciences
> University of Dundee, Dundee, Scotland, UK.
> www.jalview.org
> www.compbio.dundee.ac.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.”
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/usageconventions.html>
> 
> 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.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sleep.html>
> 
> I hope this helps,
> Elaine
> -----
> 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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