[phenixbb] phenix.hyss

Tom Terwilliger terwilliger at lanl.gov
Wed Jan 17 08:33:03 PST 2007

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:
>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 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
>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
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web 
site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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