[3DEM] model building for reference projections

[Joachim Frank]

Note that usually, such simulations don't take anamolous scattering into 
account, which is Z-specific -- the amount of amplitude contrast can be 
different for each atom in the specimen.  If the structure contains nucleic 
acids, this effect becomes important.  Simulations that take atom-specific 
anomalous scattering into account, based on Haase's tables, have been 
recently  incorporated into the SPIDER package.

--Joachim Frank.


At 03:53 AM 10/9/2005, Sharon G. Wolf wrote:
>Adam,
>HLXSIMUL, which can be found in the MRC package,
>creates simulated projection images of model helices.
>The MRC documentation explains how to use it.
>    Good luck,
>
>--Sharon Wolf
>
>_____________________________
>Sharon Grayer Wolf, PhD.
>Electron Microscopy Unit
>Weizmann Institute of Science
>Rehovot 76100 Israel
>email: <mailto:Sharon.Wolf at weizmann.ac.il>Sharon.Wolf at weizmann.ac.il
>tel:  972-8-934-4421
>fax: 972-8-934-4161
>_____________________________
>
> >>> Adam Frost <adam.frost at yale.edu> 08-Oct-05 7:30:19 PM >>>
>**** Messages to this list are automatically archived ***
>**** Please limit quoting of previous postings to the bare minimum ****
>
>I am a new member of the 3dem list. We are working on a large,
>pseudo-helical filament imaged in ice. We are struggling to index the
>helical lattice and determine the selection rule, as the FFT only has layer
>lines out to ~25 Ang from raw images. However, we think we know what the
>helical symmetry should be, both from what we know about our protein and
>from features in the FFT.
>
>I would like to build a 3D model of our expectations, in order to calculate
>projections and transforms, and then to test our assumptions by comparing
>the expected and observed ffts. I have no idea which software package would
>be best suited to building such a model, projections from it, or transforms
>of those projections. Any suggestions will be greatly appreciated.
>
>Many thanks, --Adam
>
>
>
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Joachim Frank, Ph.D.
Howard Hughes Medical Institute,
Wadsworth Center,
Empire State Plaza,
Albany, New York 12201-0509
phone: 518 474-7002
fax:  518 486-2191 
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