[phenixbb] Persistant high average B-factor.

Nian Huang huangnian at gmail.com
Thu Jun 10 13:02:53 PDT 2010


Hi Joseph,
I had a similar situation. In the end, I ended up stopping using TLS
for my structure. Do you have the same problem by just doing
individual adp refinement?

Nian

On Mon, Jun 7, 2010 at 8:52 PM, Joseph Brock <joeylives2ride at hotmail.com> wrote:
> Dear Phenix users,
>
> I am currently using version 1.6.1-353 and I'm working on a 1.7A structure
> that has refined quite well using
> Individual_sites+individual_adp(isotropic)+occupanices+TLS: Final R-work =
> 0.1776, R-free = 0.2262
>
> However, I noticed that the average B-factor reported by polygon with these
> settings was quite high ( < 0.1 of other structures with a similar
> resolution).
>
> Discovering I could not change the value of wxu_scale when using
> individual_adp+TLS, I went about trying to reduce the average B using the
> method described here:
>
> http://phenix-online.org/pipermail/phenixbb/2007-September/000511.html
>
> However,  I still can't seem to reduce the average B-factor. I've just done
> a refinement with the following non-default (extreme) target weight
> settings:
>
>   target_weights {
>     wxc_scale = 1.5
>     fix_wxc = 2
>     fix_wxu = 0.1
>    (wxu_scale = 1)
>
> But if anything, reducing wxu to such low values makes the avergae B-even
> higher while concuretnly making the gap between R-values much worse:
>
> Final R-work = 0.1602, R-free = 0.2457
>
> This suggests to me that I'm obviously over fitting the data but I'm at a
> loss on how to proceed. Should i just accept that the automatic scaling used
> for Phenix TLS wxu is doing a good job and that my structure actually does
> have an unusually high avergae B?
>
> I'm fitting two ligands into density, which is at several places ambiguous,
> so I would like the most unbiased difference density possible.
>
> Many thanks in advance,
>
> Joe.
>
>
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