[phenixbb] phenix.grow_density documentation
Pavel Afonine
pafonine at lbl.gov
Thu Aug 11 11:01:21 PDT 2011
Hi Joern,
- as Sacha mentioned (off-list), phenix.grow_density is inspired by Acta
Cryst. (1997). D53, 540-543 paper.
- 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. Attached is a PDF file 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.
- 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:
http://www.phenix-online.org/download/nightly_builds.cgi
- 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:
sphere {
center = 21.698 7.730 33.974
radius = 5
}
sphere {
center = 23.483 10.877 35.583
radius = 5
}
Let me know if you have any questions or need help with this.
Pavel.
On 8/9/11 1:47 AM, Joern Krausze wrote:
> Dear all,
>
> could anybody please provide me with a documentation for
> phenix.grow_density? I did'nt find one on the Phenix homepage or
> elsewhere
> in the depths of the internet.
>
> Thanks in advance,
>
> Joern
>
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>
> Joern Krausze
> Molecular Structural Biology
> Helmholtz Centre for Infection Research
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