[phenixbb] phenix.hyss -element for cluster...

[Thomas C. Terwilliger]

Hi Jianghai,

I think the element doesn't make much difference here at low resolution...

-Tom T

> Hi Tom,
>
> What element_symbol should I use for tantalum bromide cluster? just
> "Ta"?  How does hyss know it is a cluster, not a single atom?
>
> Jianghai
>
> On Jan 17, 2007, at 1:13 PM, Tom Terwilliger wrote:
>
>> 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
>>>>> +++++++++++++++++++++++++++++++
>>>>>
>>>>> _______________________________________________
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>>>>> 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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