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