[phenixbb] target omit map
terwilliger at lanl.gov
Thu Sep 3 12:10:06 PDT 2009
Your SA omit map should have a mean of 0, yes. Note that the SA omit
map only has meaning inside the boundaries of the omit region (as
by the map you get from the file AutoBuild_run_xx_/OMIT/
Some things to try:
1. delete the Mg-water cluster from your structure and just refine it
and look at the maps.
2. same as above, but include simulated annealing. This is another
way to get an SA-omit map
around your Mg-water cluster.
If #2 gives a very different result than the phenix.autobuild SA-omit
map, then let me know and
I will try to figure out why.
All the best,
On Sep 3, 2009, at 12:28 PM, Susan Tsutakawa wrote:
> I am trying to generate a simulated annealing omit map of a Mg-water
> cluster in the active site of my protein but when I run the SA omit
> map, I can only see the Mg when I use the Mgwater cluster as the
> target pdb.
> When I was building the model which did not have the metal present
> (phases solved by MR), I observed this Mg-water cluster in the Fo-Fc
> maps. Geometry and distance were ideal, etc. Now that I'm at the
> final stages of refinement, I would like to do a SA omit map as a
> figure for the paper. However, if I goto the lowest sigma, I only
> see the Mg. I'm using coot with the weights included to view the SA
> omit maps. I noticed that there is very little noise at the lowest
> sigma and so I'm wondering if the 0 sigma is truly 0 sigma and any
> suggestions on what to do.
> Thank you in advance.
> phenixbb mailing list
> phenixbb at phenix-online.org
Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: terwilliger at LANL.gov
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