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

Elaine Meng meng at cgl.ucsf.edu
Tue May 31 11:52:35 PDT 2016


One smallish residue-label detail.  There are options for how they are positioned relative to the residue:

0   centroid of displayed atoms (default)
1   centroid of backbone atoms
2   primary atom (e.g. CA of amino acids, C5’ of nucleic acids)

None avoids overlaps, but I prefer “2” over the default, which in my opinion maximizes the likelihood of being on top of the atoms you are trying to view.  It can be controlled with the setattr command, e.g.

setattr m residueLabelPos 2

Elaine

> On May 31, 2016, at 11:39 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Mungo,
> Unfortunately there isn’t any option to put a contrasting rectangle behind the 3D labels, and no commands for their font size and style (bold and/or italic).  The latter are set using menu: Favorites… Preferences, category: Labels.  You can change the color of the labels with commands, e.g.
> 
> color green,rl
> 
> … to make all residue labels green. 
> 
> By contrast, for 2D labels, there is command-line control font size and style and color, as well as a contrasting-rectangle option, but then no connection with the 3D structure, so you wouldn’t have the location of the residue nor its name and number.  X,Y location and text are user-specified.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html>
> 
> Given these limitations you may prefer to go back to display/undisplay or some other means of highlighting the residue such as selection.  Selection would disrupt users’ pre-existing selections (if any) and could also slow response time.
> 
> Elaine
> 
>> On May 30, 2016, at 11:37 PM, Mungo Carstairs (Staff) <g.m.carstairs at dundee.ac.uk> wrote:
>> 
>> Hi Elaine,
>> 
>> "sleep .2" works for me (I still don't get any "wait" to happen over Rest) - but I've realised there is a much better way to do what I want which is the "rlabel" / "~rlabel" command to show a residue label as I traverse the sequence / structure.
>> 
>> One question on that - interactively (in Chimera), the label shows in a nice shadowed box (a tooltip I guess), programmatically it is just the label text, which doesn't stand out too clearly against the background. Is that the best I can get for this? I don't see anything in labelopt to customize this.
>> 
>> Thanks,
>> 
>> Mungo
> 
> 
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