Dear Jalview team,
I'm re-sending this with FASTA file attachment compressed, and without
the large PDB file attachment, which can instead be downloaded from
here:
http://pdbbeta.rcsb.org/pdb/files/2QA0.pdb
We have been attempting to use Jalview v1.0 together with the bundled
Jmol viewer to explore a multiple alignment and PDB structure
simultaneously. The jnlp for our javaws is attached. We have tried the
following on Mac OSX (Snow Leopard and Lion), and keep running into
the same problems.
Using the attached FASTA alignment and PDB structure files, we
right-click on the "AAV8/1-738" row-name of the alignment, select
"Structure -> Associate structure with sequence -> From file", and
attach the PDB file to this row.
We then right-click on the same row-name, select "Structure -> View
Structure -> 2QA0", and the JMol structure window opens.
What we then have not been able to do (except once, irreproducibly!)
is get either of the following working:
- colorization of the structure consistently with the alignment
- mouseover or selection of alignment columns highlighting
corresponding residues in the structure.
Could you possibly suggest what we might need to do to get this working?
Best wishes,
Ian Holmes
Oscar Westesson
jalview.jnlp (1.25 KB)
AAV8.protpal.seqs.fa.gz (1.76 KB)
Hi Ian.
Thanks for your email. You have indeed uncovered a significant bug in Jalview !
The problem is that the alignment you are trying to view includes sequences that are all in lowercase, and when jalview computes the mapping between sequence and structure, it doesn't ignore the case of the sequence (which it should, of course). The only way you can tell something is up is by looking at the pdb-sequence alignment report shown by selecting the 'View mapping' option from the File menu, which for your sequence shows a perfect sequence-structure alignment but reports 0% for the alignment's percentage identity.
Thankfully, there is a simple workaround - simply press Cmd-A to select all the sequences, and then Cmd+right-click to open the alignment window popup menu, and select the 'To Upper Case' option from the selection->edit submenu.
I've also opened a bug about it here (http://issues.jalview.org/browse/JAL-917) so this problem should be fixed in the next (or next-but one) release.
Dear Jalview team,
I'm re-sending this with FASTA file attachment compressed, and without
the large PDB file attachment, which can instead be downloaded from
here:
http://pdbbeta.rcsb.org/pdb/files/2QA0.pdb
Thanks for your persistence. As list admin, I received all your emails - but I can imagine you were getting more than a little frustrated. We're in the progress of revamping jalview's web site, and when we move the content over, I'll make sure that we revise our instructions about submitting files in support of bug reports to include a note about the 40K attachment limit for the discussion list.
happy jalviewing!
Jim.
ps. If you'd like to be notified when the bug is fixed, simply register on our bug tracker, browse to http://issues.jalview.org/browse/JAL-917 and click on the 'Watch' link at the right hand side of the issue report page.
···
On 26/08/2011 07:26, Ian Holmes wrote:
Jim,
Thanks very much for this excellently helpful workaround.
Best wishes, Ian
···
On Fri, Aug 26, 2011 at 1:20 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
Hi Ian.
Thanks for your email. You have indeed uncovered a significant bug in
Jalview !
The problem is that the alignment you are trying to view includes
sequences that are all in lowercase, and when jalview computes the
mapping between sequence and structure, it doesn't ignore the case of
the sequence (which it should, of course). The only way you can tell
something is up is by looking at the pdb-sequence alignment report shown
by selecting the 'View mapping' option from the File menu, which for
your sequence shows a perfect sequence-structure alignment but reports
0% for the alignment's percentage identity.
Thankfully, there is a simple workaround - simply press Cmd-A to select
all the sequences, and then Cmd+right-click to open the alignment window
popup menu, and select the 'To Upper Case' option from the
selection->edit submenu.
I've also opened a bug about it here
(http://issues.jalview.org/browse/JAL-917) so this problem should be
fixed in the next (or next-but one) release.
On 26/08/2011 07:26, Ian Holmes wrote:
Dear Jalview team,
I'm re-sending this with FASTA file attachment compressed, and without
the large PDB file attachment, which can instead be downloaded from
here:
http://pdbbeta.rcsb.org/pdb/files/2QA0.pdb
Thanks for your persistence. As list admin, I received all your emails -
but I can imagine you were getting more than a little frustrated. We're
in the progress of revamping jalview's web site, and when we move the
content over, I'll make sure that we revise our instructions about
submitting files in support of bug reports to include a note about the
40K attachment limit for the discussion list.
happy jalviewing!
Jim.
ps. If you'd like to be notified when the bug is fixed, simply register
on our bug tracker, browse to http://issues.jalview.org/browse/JAL-917
and click on the 'Watch' link at the right hand side of the issue report
page.
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