[Chimera-users] Converting EM map to SAXS bead model

Tom Goddard goddard at sonic.net
Fri Oct 15 16:26:50 PDT 2010

  Hi Alexander,

   I have talked to someone (forgot name, at Grenoble EM fitting 
workshop a year ago) who was interested in computing SAXS profiles for 
EM blobs of unknown proteins and your EM2DAM program could make that 
possible.  It might also have utility in analyzing EM maps.  I wonder 
about details like how how far apart are the dummy atoms placed.  Is 
documentation for the program available?

   About 9 months ago I added to Chimera the ability to compute a SAXS 
profile from an atomic model which is then plotted against an 
experimental profile.  The idea is that you could test various atomic 
model conformations to see which is most compatible with SAXS data.  
Since then YZ in our lab has added new options and made it work using a 
web service in addition to the option of running a local program. This 
is in Chimera daily builds but not in the 1 year old Chimera 1.4 
production release.  We will have a Chimera 1.5 release soon that will 
have it.  It uses FoXS (http://modbase.compbio.ucsf.edu/foxs/about.html) 
for the profile computation.  Here's a description from the Chimera 
User's Guide of the Chimera user interface.



> Hi Tom
> First of all, thank you  very much for very helpful comments.
> Although thanks for such a nice tool as Chimera!
> The reason I was asking all questions about volume viewing and MRC
> file format is that I am developing a tool that converts
> EM density maps to dummy atom models (EM2DAM). Bead models (PDB format)
> can be used by other software to validate EM models for example.
> You can read more here:
> http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg17870.html
> I like Chimera a lot. And if you be interested in integrating/using em2dam
> (fortran90) in Chimera, let me know.
> Btw, could you comment on SAXS function in Chimera?
> Kind regards from Hamburg
> Alexander

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