[phenixbb] phenix.hyss

Tom Terwilliger terwilliger at lanl.gov
Wed Jan 17 10:13:17 PST 2007


Hi Jianghai,
Yes, looks bad.  For a cluster, run at low resolution.  Try 4 A, then 
5, then 6...
-Tom T

At 10:51 AM 1/17/2007, you wrote:
>Hi Tom,
>
>Thanks for the response.  It doesn't look like hyss has found 
>anything.  So far what I got is as following.
>
>p=016 f=000 cc=0.050 r=010 cc=0.094 [ best cc: 0.107 0.106 ]
>p=016 f=001 cc=0.056 r=010 cc=0.090 [ best cc: 0.107 0.106 ]
>...
>
>I didn't get any good CC.
>
>How to get hyss to find a heavy atom cluster, i.e. tantalum bromide 
>clusters?
>
>Jianghai
>
>On Jan 17, 2007, at 11:33 AM, Tom Terwilliger wrote:
>
>>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
>>>+++++++++++++++++++++++++++++++
>>>
>>>_______________________________________________
>>>phenixbb mailing list
>>><mailto:phenixbb at phenix-online.org>phenixbb at phenix-online.org
>>>http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>>
>>
>>Thomas C. Terwilliger
>>Mail Stop M888
>>Los Alamos National Laboratory
>>Los Alamos, NM 87545
>>
>>Tel:  505-667-0072                 email: 
>><mailto:terwilliger at LANL.gov>terwilliger at LANL.gov
>>Fax: 505-665-3024                 SOLVE web site: 
>><http://solve.lanl.gov>http://solve.lanl.gov
>>PHENIX web site: <http:www.phenix-online.org>http:www.phenix-online.org
>>ISFI Integrated Center for Structure and Function Innovation web
>>site: <http://techcenter.mbi.ucla.edu>http://techcenter.mbi.ucla.edu
>>TB Structural Genomics Consortium web site: 
>><http://www.doe-mbi.ucla.edu/TB>http://www.doe-mbi.ucla.edu/TB
>>
>>
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>
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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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