[Chimera-users] Mapping predicted secondary structure and solvent accessibility on structure or homology model?

Oliver Clarke olibclarke at gmail.com
Mon Apr 6 11:31:37 PDT 2015


I noticed that in the multalign sequence viewer, Chimera has the option to show predicted secondary structure, but it doesn’t seem to work, at least for my sequence (it seems to work initially, but when I show predicted helices/strands there is nothing to see). 

I think that incorporating modern secondary structure, solvent accessibility and disorder prediction (e.g. using JPRED, which I believe has an open API) would be a very valuable addition to Chimera for structural analysis - it would be particularly helpful for evaluating homology models and models that are based on low resolution crystallographic or CryoEM data, to pick up places where there might be a register error. Maybe this is something to consider for Chimera 2 (or maybe there is a way to load such data in now, if I could create it externally and load it in as a set of attributes…).


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