[Chimera-users] Multialign Viewer Header Definition File (UNCLASSIFIED)

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 24 11:17:52 PST 2014


Hi Sarah,
Sure thing - this may be more than you wanted, but here are a couple of examples of alignments and header files that go with them (4 files attached).  First open the alignment and then from the alignment window menu, choose "Headers... Load" and open the corresponding header file.

(1) alignment file 1bzm-others.afa and header file 1bzm-stars.hdr
This is an example with symbols.  It shows one header line named "Zn++ binding" with yellow stars in 3 positions.

(2) alignment file HIV1_REF_2008_ENV_PRO-norecomb.fasta and header file alascan-HIV1ref-cools.hdr
This is an example with quantitative values shown as histogram bar heights.  It shows two header lines with values only at certain positions.  If I remember correctly, this is the same data I used for the "Log..." headers in the figure here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavpref-analysis>

Header format description:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat>

It should just be plain text.
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 Jan 24, 2014, at 7:59 AM, Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US) wrote:
> 
> Hello,
> I would like to generate a Header Definition File to load in to Multialign Viewer. I am unclear on the format of the file though, I keep getting errors when I try to load the file in and I think it has something to do with the way I am formatting the file. Would you be able to provide an example Header Definition file?
> 
> Thank you in advance,
> Sarah Keasey
> Graduate Student
> University of Maryland, Baltimore County
> ORISE participant, USAMRIID, Fort Detrick MD 
> 
> Classification: UNCLASSIFIED
> Caveats: NONE
> 
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