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

Alex Shkumatov ashkumat at embl-hamburg.de
Mon Oct 18 09:32:10 PDT 2010

Hi Tom

Dummy atoms are placed according to pixel size. The only documentation
is available from "em2dam -help". You can get example mentioned in help from 

 I am sending you linux binary. We are not using macs here much. I hope this
is not a problem. In attachment is a test version. There are some bugs I work 
on at the moment, but feedback is very welcome. 

It is very interesting, because I developed last version of CRYSOL (2.7). I 
never used FOXS though. What you plan to do is actually validating high
resolution models (NMR or Xray). Actually how would you treat NMR models? 
Often I see that not low energy (first conformer), but other models fit
SAXS data better, or even their combination. Plausible addition to it would
be validation of EM models by first generating dummy models and then
calculating theoretical curve and fitting to experimental data. 

>      http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/saxs/saxs.htm
> l
I am actually using alpha version 1.5 (build 31455). I tried a simple test, 
namely, loaded lysozyme and fit it to experimental data. The fit is very bad! 
and why q  is plotted starting from 0.2? 

Kind regards

On Saturday 16 October 2010 01:26:50 you wrote:
>   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.
>      http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/saxs/saxs.htm
> l
>    Tom

Alexander Shkumatov, predoc -- Biological Small Angle Scattering Group
EMBL Hamburg Outstation c/o DESY -- Building 25A
Notkestraße 85 -- 22603 Hamburg -- Germany

tel:    +49 40 89902 178    fax:    +49 40 89902 149
Email: ashkumat at embl-hamburg.de
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