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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