[Chimera-users] Cando

[Elaine Meng]

Hi Poorvi,
Oh, my colleague says you were probably using the Cando DNA origami server at
<http://cando.dna-origami.org/>
I had forgotten about that server and misunderstood your question, sorry about that.

I looked at that website and the paper describing it earlier this year.  

A primer to scaffolded DNA origami.
Castro CE, Kilchherr F, Kim DN, Shiao EL, Wauer T, Wortmann P, Bathe M, Dietz H.
Nat Methods. 2011 Mar;8(3):221-9.

The paper did say that it provides a BILD (.bild) file that can be viewed in Chimera.  However, when I looked at the web site, I could not see any way to get BILD files.  In the examples, I only saw downloads for json, svg, and xml files that cannot be used in Chimera.  However, it is possible that when a job is submitted to the server, the output includes BILD.

If you don't see that kind of file, maybe you could ask the developer of the Cando server (his email is given at the website linked above) whether it is possible to get one.  If you had that type of file (named with .bild or .bld) you could just use the Chimera file menu to open it, and then view interactively.  It is basically a display format for objects, so there would not be much operations other than rotating and otherwise manipulating the view.
Best,
Elaine

On Dec 2, 2011, at 10:39 AM, Elaine Meng wrote:

> Hi Poorvi,
> Our program, UCSF Chimera, does not handle json files.  Here is a list of the UCSF Chimera file types:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
> 
> Maybe there is a different program (also named Chimera?) that is supposed to handle json files. Best,
> 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 Dec 1, 2011, at 9:05 PM, poorvi garg wrote:
> 
>> Hii..,
>> I have generated the json files by sending it to cando . The files we have generated is opened in UCSF Chimera but I am not able to perform any options or operations of the tool .
>> Could you tell me how to perform operations on bld files of the json file obtained.
>> thanks 
>> Regards,
>> Poorvi Garg
> 
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