[Chimera-users] Integrating chimera into a database

Eric Pettersen pett at cgl.ucsf.edu
Fri Aug 26 14:37:53 PDT 2016

Hi Caitlyn
	AFAIK, bfactor data does not appear in the WebGL html file, just geometry data, so I’m not sure what’s going on there.  Anyway.  I don’t have any great ideas.  One possible thing is that you create one or more scenes showing various relevant positions of your structure, with labels, and then save them as an HTML “storyboard”:

http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/animation/frameanimation.html (click on “Storyboard” on the left).

The scenes will be shown as thumbnails across the top, and a larger version of whichever one is chosen will be shown below, complete with labels.  Just above the large image will be a “Load 3D Data” button which will allow the scene to be manipulated, just like the WebGL version, though labels will disappear (until the image is reloaded).

Like I said, not great, but maybe it’s something.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Aug 25, 2016, at 9:28 AM, McCafferty, Caitlyn (NIH/NEI) [F] <caitlyn.mccafferty at nih.gov> wrote:
> Hi Eric, 
> Thank you for your quick response. I really want the labels for the amino acids to be present. I tried adding labels in the session and exporting to the html file and like you said no labels appeared. I did, however, notice that data that I added to the B-factor column appeared in the html file. Would it be possible to add the labels to another column and have them show up? Or do you have any other suggestions on how to approach this issue?
> Thank you for your time,
> Caitlyn McCafferty
> Postbaccalaureate Fellow
> Ophthalmic Genetics and Visual Function Branch
> National Eye Institute
> Bldg. 10 Rm. 6-3350
> Tel: (301) 402-7058
> Email: caitlyn.mccafferty at nih.gov <mailto:caitlyn.mccafferty at nih.gov> 
> From: Eric Pettersen [pett at cgl.ucsf.edu]
> Sent: Monday, August 15, 2016 8:26 PM
> To: McCafferty, Caitlyn (NIH/NEI) [F]
> Cc: chimera-users at cgl.ucsf.edu BB
> Subject: Re: [Chimera-users] Integrating chimera into a database
> Hi Caitlyn,
> Another possible option to be aware of is that Chimera can export to WebGL format, which can show the 3D structure in most modern web browsers and allow it to be manipulated with the mouse much in the same way it can in Chimera’s graphics window.  Well, rotation and scaling at least.  You can export to WebGL either with File…Export, or with the “export” command.
> The WebGL does lack some basic things, like showing text labels, so you would really need to try it out to see if it meets your needs.
> —Eric
> Eric Pettersen
> UCSF Computer Graphics Lab
>> On Aug 15, 2016, at 4:49 PM, Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
>> Hi Caitlyn,
>> The users would have to have Chimera installed on their machines in order to open Chimera sessions.  There is a “web data” mechanism for the browser to use Chimera as a helper app (analogous to Preview or Adobe for PDF files), but it requires Chimera on the end machine.
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.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 Aug 15, 2016, at 8:14 AM, McCafferty, Caitlyn (NIH/NEI) [F] <caitlyn.mccafferty at nih.gov <mailto:caitlyn.mccafferty at nih.gov>> wrote:
>>> Hi, 
>>> I have a number of colored protein structures from chimera that are saved as python files. I would like to put these structures on a database so other users may access them. Is there a way (preferably using html) that a user could click on the python file and it would open up in chimera through the database-- even if the user does not have chimera installed?
>>> Thank you,
>>> Caitlyn McCafferty
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