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

[Eric Pettersen]

On Apr 6, 2015, at 11:31 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi,
> 
> 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). 

It is possible that it predicts no helices or sheets for your sequence, but that would be unusual.  If you send me the sequence, I'll investigate.

> 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…).

Well, at the time I added the feature I wanted something I could directly include in Chimera and that would provide immediate feedback (i.e. didn't take minutes to execute).  The GOR algorithm fit those criteria, those it certainly isn't state of the art for the field.  I would consider a JPRED option for Chimera 2 (though it meets neither of the criteria I mentioned), but probably not Chimera 1 for now.

You could load attribute data into the residue with the defattr command, or if you're just looking at a single sequence you could make a custom header for that sequence (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/defineheader.html).

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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