Hi Bob. I'm also interested, though I think you should be aiming big ;)
The development build of Jalview (which will eventually be 2.8.2 by the summer) has an RNAView based secondary structure shading scheme that was developed by a summer student, Anne Menard, back in 2012. Currently, 2.8.2 uses Fabrice Jossinet's RNAView service to process the RNA chains, but it would be great if similar functionality were built in to Jmol, since Jalview 2.8.2 already uses DSSP assignments. Try loading PDB 2GIS into Jalview via its sequence fetcher, you can then open a Jmol view and a VARNA view, and also shade the sequence by RNA sugar edge interactions (Leontis/Westhoff/Hoogstein 2.5D annotation). Jim. On 09/04/2014 09:22, Angel Herráez wrote: > Bob and Xiang-Jun, > > That sounds VERY interesting! > Congratulations > > I will need some time before I can test this at some length. > > Yes, avoid the ribosome. I have a small set of PDB IDs that could be > used for testing/demo, if you need them -- tRNA, snall and large > rRNA, hairpins, an N base bound to a small RNA (riboswitch)... > > By the way, although this is separate, we recently had some problem > (while testing some Proteopedia issues) with individual nucleotides > (GMP, ATP...) being read as "nucleic" rather than "ligand". I > understand the rationale, but it is not ideal. That might also affect > when you start doing fancy nucleic secondary structure rendering. > > > > > > > ------------------------------------------------------------------------------ > Put Bad Developers to Shame > Dominate Development with Jenkins Continuous Integration > Continuously Automate Build, Test & Deployment > Start a new project now. Try Jenkins in the cloud. > http://p.sf.net/sfu/13600_Cloudbees > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
