[Chimera-users] Web Access Data

[Elaine Meng]

Hi Thiru,
The easy way to tell if a chimerax file is OK is to just try opening  
it in Chimera with File... Open (file type could be "all (guess type)"  
or "Chimera web data").

The format is described here:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html 
 >

The "name" is the name to use for the local copy of the file from the  
web, and "loc" is where it is on the web.  So "name" is not that  
important except that it should be the right type (if the file is  
python, the name should end in .py).  As far as I can tell, your  
chimerax file looks OK.

If opening the chimerax file directly in Chimera works OK, but  
clicking the link on your web page doesn't, your webmaster may need to  
change a server setting:  the MIME type application/x-chimerax should  
be mapped to the extension .chimerax in the server configuration file.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Mar 31, 2009, at 11:47 AM, Thiruvarangan Ramaraj wrote:

> Hi Elaine,
>
> Thanks for your help. I know it is a delayed response, I did not get  
> a chance to have a look at it. I am trying to spend some time now on  
> web access data.
>
> So, following your instructions, I created a session in chimera and  
> saved it as a python session, 1A14AgSurface.py
>
> I was looking at the chimerax file, it had
>
> <file name="session.py" format="text" loc="http://sfld.rbvi.ucsf.edu/data/site_sessions/1yey.py 
> "/>
>
> it has two .py files, I am little confused about session.py and  
> 1yey.py
>
> Here is the 1A14Ag.chimerax file that I have
>
> <?xml version="1.0"?>
>   <ChimeraPuppet type="std_webdata">
> <web_files>
>   <file  name="1A14AgSurface.py" format="text" loc="http://www.cs.montana.edu/~tramaraj/Research/1A14AgSurface.py 
> "/>
> </web_files>
>   </ChimeraPuppet>
>
> I am not sure if I have the file tag written correctly.
>
> In my website, I would have something like the following
> <a href="1A14Ag.chimerax"> <img src="1A14AgSurface.png"> </a>
>
> Any help would be greatly appreciated.
>
> Thank you for your
>  time and help
>
> Sincerely
>
> Thiru R
>
>
>
>
>
>
> --- On Tue, 3/3/09, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Web Access Data
> To: thiruvaranganr at yahoo.com
> Cc: chimera-users at cgl.ucsf.edu
> Date: Tuesday, March 3, 2009, 10:10 AM
>
> Hi Thiru,
> The session file is python (*.py) ... you cannot just rename it as  
> *.chimerax.
> Instead you would make a chimerax file that gives the names/ 
> locations of any
> files you want to open in Chimera, such as the python session file,  
> and can
> include various Chimera commands.  If all you want to do is open the  
> session,
> the chimerax file will be very simple.
>
> For example, these 6 lines of text are a chimerax file from the
> Structure-Function Linkage Database
>  (SFLD):
>
> <?xml version="1.0"?>
>   <ChimeraPuppet type="std_webdata">
> <web_files>
>   <file  name="session.py" format="text"
> loc="http://sfld.rbvi.ucsf.edu/data/site_sessions/1yey.py"/>
> </web_files>
>   </ChimeraPuppet>
>
> Your web page would link to the chimerax file.  Then when the  
> chimerax file is
> opened by Chimera, Chimera will get the session file named inside.
>
> The page at the SFLD that has this link is
> <http://sfld.rbvi.ucsf.edu/cgi-bin/SFLDvm.py?view=family&id=111>
> The chimerax file is linked to the large "Active Site" image.
>
> You can test your chimerax file without using the web just by  
> opening it in
> Chimera.  Then if it works, you can link it to a web page, but there  
> is one more
> step:
>
> If you are using a cgi-bin script to create the chimerax files on  
> the fly, the
> cgi-bin script must specify the Content-type header as application/x- 
> chimerax.
>
> If you just have pre-made chimerax files, your webmaster needs to  
> change the web
> server settings so that it sends this information along with the file.
>
> The chimerax format is described here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html 
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
>
>
>
>
> On Mar 2, 2009, at 6:46 PM, Thiruvarangan Ramaraj wrote:
>
> > Hello All,
> >
> > I created a session and saved it under .chimerax extension. I have  
> a link
> > to this session on a web page. When I click on this link I wanted  
> the
> > session to open directly using the chimera program.
> >
>
> >
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.html#webdata
> >
> > I tried to follow the instructions given in the above link, still  
> I am
> unsuccessful in figuring it out.
> >
> > Any suggestions/ideas would be greatly appreciated.
> >
> > Thank You
> >
> > Thiru
> >
> > _______________________________________________
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>
>