Dear developers
I would like to visualize a sequence alignment (previously created by clustalw in a folder "ALN/") and to link each
sequence to its own pdb file (all the structural models are stored in a "PDB/" folder).
Suppose I have two sequences seqA and sebB, whose alignment is ALN/tmp.aln and whose models are PDB/seqA.pdb
and PDB/seqB.pdb.
I'm using this syntax:
<applet code="jalview.bin.JalviewLite" width="100%" height="330" archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
<param name="file" value="TMP/tmp.aln">
<param name="PDBFile" value="PDB/seqA.pdb TMP/seqA">
<param name="PDBFile2" value="PDB/seqB.pdb TMP/seqB">
<param name="label" value="Jalview">
<param name="embedded" value="true">
<param name="RGB" value="CCCC99">
</applet>
When I open the HTML page, two Jmol popup are automatically launched.
If I close one or both, I cannot open again none of them from the Jalview applet.
Can you suggest me if I'm wrong?
Probably I'm not mapping properly structures to aligned sequences.
Another short question: Is there any way for avoid the popups?
With best regards,
Matteo Floris
···
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Matteo Floris, Ph.D.
CRS4 - Biomedicine Sector
Center for Advanced Studies, Research and Development in Sardinia
Technology Park Polaris - Building 1
Piscina Manna, 09010 Pula (CA) - Italy
phone +39 070 9250 1
mobile +39 333 48 57 679
email: floris@crs4.it, matteo.floris@gmail.com
web: http://www.crs4.it
It is not from the benevolence of the butcher, the brewer, or the
baker, that we expect our dinner, but [...]. [Adam Smith]
Hi there, Matteo.
Suppose I have two sequences seqA and sebB, whose alignment is
ALN/tmp.aln and whose models are PDB/seqA.pdb
and PDB/seqB.pdb.
I'm using this syntax:
<applet code="jalview.bin.JalviewLite" width="100%" height="330"
archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
<param name="file" value="TMP/tmp.aln">
<param name="PDBFile" value="PDB/seqA.pdb TMP/seqA">
<param name="PDBFile2" value="PDB/seqB.pdb TMP/seqB">
<param name="label" value="Jalview">
<param name="embedded" value="true">
<param name="RGB" value="CCCC99">
</applet>
When I open the HTML page, two Jmol popup are automatically launched.
If I close one or both, I cannot open again none of them from the
Jalview applet.
Can you suggest me if I'm wrong?
Probably I'm not mapping properly structures to aligned sequences.
Your suspicions are correct. Assuming your sequences have IDs like 'seqA' and 'seqB' then try using PDBFile lines like:
<param name="PDBFile" value="PDB/seqA.pdb seqA">
<param name="PDBFile2" value="PDB/seqB.pdb seqB">
The popup Jmol views will still appear, but they should be coloured according to their associated sequence. Try using the 'debug' parameter to check that the PDB association is happening, too.
Another short question: Is there any way for avoid the popups?
Not in the stable version (2.6.1) - but I'm currently working on an example for version 2.7 where a Jmol and JalviewLite are embedded on the page. You can see the prototype here:
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/applet/embeddedWJmol.html
It's still a bit flaky (mostly due to the page layout - but there will also be some browser issues, I suspect) - but should give you an idea of what the next version will allow. Bug reports gratefully received at http://issues.jalview.org/browse/JAL-621
Jim.
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On 11/07/2011 14:42, Matteo Floris wrote: