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.ht...

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@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@cgl.ucsf.edu> wrote: From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Web Access Data To: thiruvaranganr@yahoo.com Cc: chimera-users@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.ht...

...

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@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.htm...

...

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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