[Chimera-users] 'Automatically' annotate multiple structures

Conrad Huang conrad at cgl.ucsf.edu
Mon Feb 26 10:58:28 PST 2018


Hi, Joe.

I added a "label" option to the "tile" command so you can add 2D labels 
for tiled models with:

tile #0 label true

(Unfortunately, the model specifier is required.)  This will display the 
model number and name at the lower left corner of each tile.  The label 
styles can be changed using the "2dlabel" command, e.g.,

2dlabel change * color cyan

Of course, there are limitations since the 2D labels are not associated 
with the models, so scaling and translating models will not affect the 
added labels and generally resulting in an unusable view; rotating 
models should be okay though.

This should be available in Chimera daily builds dated February 27, 2018 
or later.  Hope this helps a little.

Conrad

On 2/24/2018 10:18 AM, Healey, Joe wrote:
> Hi Elaine,
> 
> Ah I didn’t realise it was fractional. I thought the model x and y might 
> in some way be translatable to the viewer x and y.
> 
> If it’s beyond the scope of Chimera to do this easily I might be able to 
> come up with a different approach when I just put the final figure together.
> 
> Thanks for your help anyway!
> 
> Joe
> 
> __
> 
> M.Sc. B.Sc. (Hons) MSRB
> 
> PhD Student
> 
> MOAC CDT, Senate House
> 
> University of Warwick
> 
> Coventry
> 
> CV47AL
> Mob: +44 (0) 7536 042620 <tel:+44%207536%20042620>  | 
>   Email:J.R.J.Healey at warwick.ac.uk <mailto:J.R.J.Healey at warwick.ac.uk>
> 
> Jointly working in:
> 
> Waterfield Lab 
> <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/>(WMS Microbiology 
> and Infection Unit)
> 
> and the Gibson Lab 
> <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick 
> Chemistry)
> 
> Twitter:@JRJHealey <https://twitter.com/JRJHealey>  |  Website:MOAC Page 
> <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | 
> ORCID: orcid.org/0000-0002-9569-6738 <http://orcid.org/0000-0002-9569-6738>
> 
> 
> On 23 Feb 2018, at 19:07, Elaine Meng <meng at cgl.ucsf.edu 
> <mailto:meng at cgl.ucsf.edu>> wrote:
> 
>> Hi Joe,
>> I don’t think there is a simple way (not involving python scripting) 
>> to achieve what you want…
>>
>> The instructions in that previous post are for 3D labels, not 2D, and 
>> they work to label the first atom in each structure by the model number:
>>
>> labelopt info molecule
>> la @/serialNumber=1
>>
>> The part that specifies model number is “info molecule” and it does 
>> not have a model-name option. I see that “molecule” isn’t even 
>> documented as a choice for type of info, so I will need to add it… 
>> apparently I didn’t know about it and failed to notice the omission 
>> when that previous post appeared!  Sorry about that.  IMO, “molecule” 
>> is somewhat misleading and should be “model” instead, as there could 
>> be many different molecules in a single model.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/labelopt.html>
>>
>> Don’t be distracted by the serial number stuff in the “label” command; 
>> it simply indicates which atoms to label: the first one in each model. 
>>  It was used simply to just get one label per model without prior 
>> knowledge of the atom names and residue numbers in each structure, 
>> since the label command potentially applies to all atoms.
>>
>> You could use the “2dlabels” command instead, but you would have to 
>> manually specify the text for each label and its X,Y position in the 
>> graphics window (or use the 2D Labels graphical interface and place 
>> the labels by hand, which is much easier as long as you don’t have to 
>> do it too many times)
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html>
>>
>> Somebody else would have to advise on the Python-scripting 
>> possibilities for a more automatic approach.
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>> On Feb 23, 2018, at 1:54 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk 
>>> <mailto:J.R.J.Healey at warwick.ac.uk>> wrote:
>>>
>>> Hi again Chimera team,
>>> I'm looking for a fairly quick and dirty way to apply some 
>>> annotations using 2D labels to a bunch of open structures.
>>>
>>> Basically, I have ~16 structures open on screen, which I then tile to 
>>> compare. I'd like the model name to be displayed just below each 
>>> model so that its easy to track. I've found this thread 
>>> (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-July/004081.html) 
>>> which appears to be attempting a similar thing (though I'd like to 
>>> use the model.name not serial number), but the approach doesn't seem 
>>> to work (no labels appear and there is no information in the reply 
>>> log or IDLE to give me any clues).
>>>
>>> Any suggestions/alternatives appreciated!
>>> Joe
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



More information about the Chimera-users mailing list