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<div class="moz-text-flowed" style="font-family: -moz-fixed;
font-size: 12px;" lang="x-unicode">Hi Joern,
<br>
<br>
- as Sacha mentioned (off-list), phenix.grow_density is inspired
by Acta Cryst. (1997). D53, 540-543 paper.
<br>
<br>
- sorry for the lack of documentation. This is one of the (10+)
(slow) on-going projects that we still need work on in order to
make it more automated and user-friendly. Here is a PDF file
(<a class="moz-txt-link-freetext" href="http://cci.lbl.gov/~afonine/tmp/grow_density.pdf">http://cci.lbl.gov/~afonine/tmp/grow_density.pdf</a>) that I wrote
for Sacha to explain some parameters of phenix.grow_density. It is
very sketchy and may not be 100% up-to-date, but I hope it helps.
<br>
<br>
- the error message you get ("Refinement failed... ) is actually a
bug - sorry. I am fixing it right now and the fixed version will
be available in the next nightly build of PHENIX available in a
day of two here:
<br>
<a class="moz-txt-link-freetext"
href="http://www.phenix-online.org/download/nightly_builds.cgi">http://www.phenix-online.org/download/nightly_builds.cgi</a>
<br>
<br>
- I recall, defining several spheres where the DA are going to be
placed is better than defining one large sphere, although it
depends on the region size and shape. For example:
<br>
sphere {
<br>
center = 21.698 7.730 33.974
<br>
radius = 5
<br>
}
<br>
sphere {
<br>
center = 23.483 10.877 35.583
<br>
radius = 5
<br>
}
<br>
<br>
Let me know if you have any questions or need help with this.
<br>
Pavel.
<br>
<br>
On 8/9/11 1:47 AM, Joern Krausze wrote:
<br>
<blockquote type="cite" style="font-size: large; color: rgb(0, 0,
0);">Dear all,
<br>
<br>
could anybody please provide me with a documentation for
<br>
phenix.grow_density? I did'nt find one on the Phenix homepage or
elsewhere
<br>
in the depths of the internet.
<br>
<br>
Thanks in advance,
<br>
<br>
Joern
<br>
<br>
******************************************
<br>
Address:
<br>
<br>
Joern Krausze
<br>
Molecular Structural Biology
<br>
Helmholtz Centre for Infection Research
<br>
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<br>
38124 Braunschweig
<br>
Germany
<br>
<br>
Email: <a class="moz-txt-link-abbreviated"
href="mailto:joern.krausze@helmholtz-hzi.de">joern.krausze@helmholtz-hzi.de</a>
<br>
Phone: +49 (0)531 6181 7023 (office)
<br>
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<br>
******************************************
<br>
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href="http://www.helmholtz-hzi.de">www.helmholtz-hzi.de</a>
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