[Chimera-users] Automatic setting of suggested contour level

Tom Goddard goddard at sonic.net
Wed Nov 27 14:01:48 PST 2013


Hi Darrell,

  Chimera could fetch the EMDB XML metadata file and extract the suggested contour level and use it.  I have noticed that the suggested levels are sometimes very wrong, deep in the noise.  Some investigation will be needed to see if the levels are right often enough to be usable.  I've made a Chimera feature request entry in our database.

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12644

It would be a good feature for Chimera 2 which we are working on but is probably a year or more away.  I'm spending most time on our next generation Chimera 2 rather than adding features to the current Chimera 1.

	Tom


On Nov 27, 2013, at 11:51 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote:

> Hi Chimera team,
> 
> I love how Chimera seems to intelligently and automatically choose a contour level for fetched EMDB files. However, I have noticed that most EMDB files have a "suggested contour level" associated with them. It can be obtained in the "header" XML files under the tag <contourLevel>. How much more work would it be to automatically fetch this information when fetching the map and then set the contour level to the recommended setting? Would you consider doing it?
> 
> Thanks,
> Darrell
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
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