[phenixbb] phenix.hyss

[Jianghai Zhu]

The MAD data only goes to 4 A.  I tried SOLVE and based on the CC  
table output from SOLVE, the anomalous signal goes to 4.3 A.  I  
believe the cut of CC in SOLVE is 0.3.  Unfortunately,  the native  
data is not isomorphous.

Jianghai

On Jan 17, 2007, at 1:17 PM, Peter Zwart wrote:

>> 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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>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>
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