[Chimera-users] Map conservation of my sequence compared to sequence alignment

Jim Procter jprocter at compbio.dundee.ac.uk
Mon Jan 9 01:42:22 PST 2017

Hi Matthias - and apologies for the shameless plug, Elaine!

On 06/01/2017 15:59, Elaine Meng replied you Matthias Fellner:
>> I have the consensus mapped onto my protein but that is not what IÂ want. IÂ want to show how the residues of my protein are conserved. For example at a particular residue the consensus is a C but in my structure its a W. at the moment the W is colored to be highly conserved based on the consenus of the C. The W is maybe 15% conserved, how can IÂ map the conservation of my sequence compared to all the other sequences.

You can do this if you first open your alignment in Jalview. All you
need to do is set your structure to be the 'reference sequence'
(http://www.jalview.org/help/html/calculations/referenceseq.html). It
will then be used insead of the consensus sequence when computing
computing blosum62 and PID shading.

After that, just make sure Chimera configured as your structure viewer
(http://www.jalview.org/help/html/features/chimera.html), and right
click on the 'View structure...' dialog to load your structure. Jalview
will open the structure coloured according to the sequence. We have a
training video here: https://youtu.be/5wNrCcTbbyg

Hope this helps!

Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

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