[phenixbb] phenix.grow_density documentation

[Pavel Afonine]

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. Here is a PDF file 
(http://cci.lbl.gov/~afonine/tmp/grow_density.pdf) 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
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