Jalview tutorial at VIZBI - March 19th 2011

Jalview Discussion
1

Dear US/Boston area Jalview users!

There is an opportunity for you to attend a Jalview tutorial as part of
the first Visualization of Biological Data (VIZBI) tutorial day, which
takes place at the Broad Institute on March 19th, 2011.

The VIZBI tutorial day is separate to the main VIZBI 2012 event, and
provides the opportunity for people to learn how to use state of the art
tools for biological data visualization and apply them to their own
data. Registration for the day costs $75, and participants should select
one 3 hour tutorial to attend in the morning (see
http://vizbi.org/2011/Program/Saturday/ for the full list). The
afternoon session is unstructured, and provides the opportunity for you
to try out your newly acquired visualization skills with your own data,
with all the tutors on hand so you can discuss specific problems.

If you are interested in attending the tutorial day, you can register at
http://vizbi.org/2011/Registration/

Should there be sufficient interest, I will be running a shortened
version of the one day Jalview tutorial, and am happy to take requests
on which areas of Jalview are of most interest to participants. Please
get in touch directly if you'd like to suggest some topics.

Happy Jalviewing, and I look forward to meeting some of you in Boston
this March!
Jim Procter.

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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

2

Hello,
I've just ran into a bug with the latest jalview version. As I mentioned in a previous report I try to reedit my previous projects so that they work with the latest jalview version.
Everything worked fine until I tried to bind two sequences coming from two different alignments to one 3D structure file :
- one alignment is antibody heavy chains
- the other is antibody light chains
- the 3D is an antibody pdb file
When the view structure is selected, jalview offers to reuse the currently displayed structure for the second sequence. Then when hovering over a residue in the sequence file, the same residue is highlighted in the display (that's the expected behavior and it proves that some binding actually occurs). But when the color by sequence option is picked, only the first sequence's color is actually transferred to the model.
-Paul

3

Hi Paul.

Hello,
I’ve just ran into a bug with the latest jalview version. As I mentioned in a previous report I try to reedit my previous projects so that they work with the latest jalview version.
Everything worked fine until I tried to bind two sequences coming from two different alignments to one 3D structure file :

  • one alignment is antibody heavy chains
  • the other is antibody light chains
  • the 3D is an antibody pdb file
    When the view structure is selected, jalview offers to reuse the currently displayed structure for the second sequence. Then when hovering over a residue in the sequence file, the same residue is highlighted in the display (that’s the expected behavior and it proves that some binding actually occurs). But when the color by sequence option is picked, only the first sequence’s color is actually transferred to the model.
    Yes - I’m actually working on a jalviewLite visualisation where this
    is an issue, too. The problem is that whilst Jalview 2.6 allows
    many:many relationships between structures in a Jmol view and any
    sequences appearing in any alignments, the mechanism that colours the
    structures by their associated sequences only holds a reference to a
    single alignment, which is obviously not sufficient. I’ll hopefully
    have this resolved for the next release.

Jim.