[Chimera-users] Add secondary structure or symbols to headers of multalign viewer (sequence)

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 31 08:00:40 PDT 2017


Dear Liuqing Chen,
We don’t have secondary structure symbols, but there are other symbols as shown in the figure in this section of the manual page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers>

The definition file format is fully described here, and it is a simple text file that you can easily make by typing into your favorite text-editing program.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat>

As it says, the shapes are circle, square, diamond and star.  The only tricky thing is that the data lines have tabs in them, which is why I don’t just show a 3-line example file right in this e-mail. I attached one (simple.hdr) so you can see how simple it is.  but you have to first open some sequence or alignment and then open this definition file ( sequence window menu: Headers… Load). It will show a blue star at the 3rd position of the sequence or alignment, as in the attached image. 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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: simple.hdr
Type: application/octet-stream
Size: 46 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170331/e85cb020/attachment-0001.obj>
-------------- next part --------------

-------------- next part --------------
A non-text attachment was scrubbed...
Name: starheader.png
Type: image/png
Size: 70855 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170331/e85cb020/attachment-0001.png>
-------------- next part --------------
> On Mar 30, 2017, at 7:51 PM, 陈柳青 <519198561 at 163.com> wrote:
> 
> Dear all !
> Is it possible to add secondary structure or symbols to multalign viewer headers?  I know can use "alignment header definition files"  do this ,  but  i don't know how to make the definition files,  anyone can give me these files  or tell me how to do it?
> thanks!
> Liuqing Chen



More information about the Chimera-users mailing list