[phenixbb] phenix.hyss

[Jianghai Zhu]

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
>> 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: 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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