[phenixbb] phenix.hyss

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Wed Jan 17 11:22:09 PST 2007

Hi Jianghai,

I think the large memory consumption is due to the large number of
triplet phase relations. Using the --real_space_squaring option may

> The MAD data only goes to 4 A.  I tried SOLVE and based on the CC
> table output from SOLVE, the anomalous signal goes to 4.3 A.  I
> believe the cut of CC in SOLVE is 0.3.  Unfortunately,  the native
> data is not isomorphous.

Finding 50 Se given only 4.3 A resolution is difficult. I'm sorry
to say I'm not very hopeful, but I'd try all tools out there.
I'd also play with the resolution cutoff. hyss used 4 A in your case.
I'd try 4.5 and maybe even all cutoffs 4.4, 4.3, 4.2, 4.1 if you
can afford the CPU time, with --real_space_squaring first, without
it if nothing worked still.

Another question is the space group. You cannot distinguish I222
and I212121 from the systematic absences. Are you certain it is

To find a cluster, lower the resolution significantly. I've had success
with 6 A cutoff (--resolution=6). The atom type doesn't really matter,
Ta should be fine. If it works, hyss will give you atoms around the
centers of the clusters. You have to fit the whole cluster yourself.
I'm not sure about the best approach for this (inspecting the map with
coot and place the cluster manually?). Maybe someone else can help?

How many clusters do you expect? In general, the more you expect the
more data you need. I.e. a 6 A cutoff may work for finding a couple
of sites, but for say 10 sites you'd need 5 A. -- These numbers
are just to convey the idea. What works exactly depends highly on
the available data.

Hope this helps.


More information about the phenixbb mailing list