Dear Dirk

You might find one of the programs mentioned by Andreas below useful for your purpose.


Am 28.07.2010 um 18:26 schrieb Andreas Förster <>:

Here's a preliminary summary of the suggestions I got from the ccp4 community regarding the problem stated below (calculate theoretical SAXS data from EM reconstruction):

The program em2dam, currently developed at EMBL-Hamburg (where the magicians of SAXS live), converts a Spider map into a pdb file, which can then be used as input for another EMBL-Hamburg program, crysol. This approach does what I want. Nice. Em2dam hasn't been released yet, but is available for testing upon request ( ).

HYDRO can also calculate scattering form factors from dummy-bead models, but I didn't try that out. From the group that wrote HYDRO comes hydromic, a program that calculates, from an EM map, a distance distribution and a P vs. h list whose usefulness didn't immediately reveal itself to me. Those more familiar with SAXS might find that this program is just what they want.

The program vol2pdb, which is part of the situs package, converts spider format em maps to dummy-bead models. I couldn't suppress the feeling that the pdbs obtained with em2dam were closer to the truth. Situs also has a SAXS tutorial that might be useful.

The EMAN program proc3d with the calcsf option can calculate scattering curves. The output file contains the F**2/s distribution for the map with max=0.0. Some scaling might be required. I didn't try this.

Chimera might have a SAXS function.  I didn't check.

Thanks to all who contributed ideas and suggested approaches, and special thanks to Alex for sharing em2dam.


On 23/07/2010 11:54, Andreas Förster wrote:
Dear all,

the other day I obtained SAXS data from which a low-resolution
structural model was calculated. The model is simpler/less complex than
one of the same protein that we obtained with cryo-EM.

Is there a way to estimate theoretical SAXS data from a cryo-EM
reconstruction to compare with the obtained raw data? Is there a program that does for a reconstruction what CRYSOL does for pdbs? I understand that there would be a huge amount of handwaving involved, but it might
help us reconcile our models.



      Andreas Förster, Research Associate
      Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London

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