Hello Jim, thank you for your explanations! Now I am able to display consensus logo. In regard to secondary structures, i don't have neither PDB files nor secondary structure annotations..... Since for the moment our program aligns all protein sequences (selected for a certain modification) it can found on a web site, we have not thought to include secondary structure information, and we thought this was something "automatic" for jalview (to find in web secondary structure). Anyway, we are thinking how to modify our program to include secondary structure. As soon as we will have either PDB or annotation I think I will come back to you.....
In the meanwhile, thank you again. Alessandra 2015-06-15 20:16 GMT+02:00 Jim Procter <[email protected]>: > Hello Alessandra > > On 15/06/2015 12:51, Alessandra Gastaldello wrote: > > > > I would like to have in the images also the SECONDARY STRUCTURE > > ANNOTATION and THE LOGO on CONSENSUS HISTOGRAMS. > > > > I can't figure out how to do this... > > > > I am thinking that maybe I would have to add some parameters in the > > Jalview properties file. > You're correct, though you may also need some additional data: since you > can only display secondary structure annotation if you actually have > some secondary structure information for sequences. Jalview can extract > those data automatically from 3D structure, but to do that you'll need > to have the PDB files available for your sequences. Alternately, if you > have secondary structure annotation, you could turn them into Jalview > annotation files. Which do you prefer here ? > > Modifying the properties to get the layout/visualisations you need for > batch mode. > The easiest way to do this is to launch Jalview in interactive mode with > the '-props' argument pointing to a copy of your current jalview > properties file. Then configure the default annotation options via > Tools->Preferences so that consensus sequence logos are displayed > automatically. > > For what you want, though - the relevant property line for showing > consensus logos is: > SHOW_CONSENSUS_LOGO=true > > Let me know what you want to do about secondary structure annotation... > if you have annotation available it might be easiest to create an > importer with a groovy script. > Jim. > > _______________________________________________ > Jalview-discuss mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss >
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