[phenixbb] phenix.hyss

[Peter Zwart]

> 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 ]

This indeed doesn't look very promising.
Do you have any reasonable anomalous differences? Check the 
measurability table/graph from mmtbx.xtriage or look at the anomalous 
correlations with iotbx.reflection_statistics.

If you are looking for clusters, you might want to lower the resolution 
to something like 4 A or so. Do you have any native data that might do 
you any good?

Cheers

Peter




> 
> 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 <mailto: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 
>> <mailto: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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> 
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