Thanks for the response. It doesn't look like hyss has found
anything. So far what I got is as following.
...
I didn't get any good CC.
How to get hyss to find a heavy atom cluster, i.e. tantalum bromide
Hi Jianghai,
Maybe Ralf will reply to you too, but this sounds way too long. Have
a look at the output of hyss...and compare with the one below:
A good output:
f = peaklist index in two-site translation function
cc = correlation coefficient after extrapolation scan
r = number of dual-space recycling cycles
cc = final correlation coefficient
...
p=001 f=001 cc=0.088 r=010 cc=0.127 [ best cc: 0.144 ]
p=001 f=002 cc=0.079 r=010 cc=0.138 [ best cc: 0.144 0.138 ]
Number of matching sites of top 2 structures: 2
p=002 f=000 cc=0.074 r=010 cc=0.141 [ best cc: 0.144 0.141 ]
Number of matching sites of top 2 structures: 2
...
p=010 f=001 cc=0.085 r=010 cc=0.119 [ best cc: 0.333 ]
p=010 f=002 cc=0.110 r=010 cc=0.339 [ best cc: 0.339 0.333 ]
Number of matching sites of top 2 structures: 45
A bad one would look just like this good one except there would be a
long list of correlations, and none would be very high. An ok
correlation is 0.3, good is 0.4 or more bad is 0.2 or less.
The run above with 50 sites took 11 minutes...
-Tom T
At 08:48 AM 1/17/2007, you wrote:
Hi,
I am trying to use phenix.hyss to find 50 Se sites from my MAD
data. Phenix.hyss has been running for more than 24 hrs now and is
still going. I have 4 GB memories on my workstation. Phenix.hyss
used more 95% of it and makes the machine basically unusable
now. Is it normal for phenix.hyss to use so much memories? I am
using Phenix 1.24.1b.
Jianghai
+++++++++++++++++++++++++++++++
Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3232
+++++++++++++++++++++++++++++++
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email:
Fax: 505-665-3024 SOLVE web site:
ISFI Integrated Center for Structure and Function Innovation web
TB Structural Genomics Consortium web site:
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