Dear Dirk
You might find one of the programs mentioned by Andreas below useful
for your purpose.
Cheers
Alex
Am 28.07.2010 um 18:26 schrieb Andreas Förster <[log in to unmask]>:
> 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 ([log in to unmask]
> ).
> http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html
>
>
> 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.
> http://leonardo.fcu.um.es/macromol/programs/programs.htm
>
>
> 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.
> http://situs.biomachina.org/tutorial_saxs.html
>
> 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.
> http://blake.bcm.tmc.edu/eman/
>
> Chimera might have a SAXS function. I didn't check.
> http://www.cgl.ucsf.edu/chimera/
>
> Thanks to all who contributed ideas and suggested approaches, and
> special thanks to Alex for sharing em2dam.
>
>
> Andreas
>
>
>
> 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.
>>
>> Thanks.
>>
>>
>> Andreas
>>
>>
>
> --
> Andreas Förster, Research Associate
> Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
> http://www.msf.bio.ic.ac.uk
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