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! Jim. -- ------------------------------------------------------------------- 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