[phenixbb] chain definition in phenix

[Paul D. Adams]

Hi Kornelius,

   which version of PHENIX are you using?

   Cheers,
	Paul

On Dec 18, 2007, at 11:26 AM, Kornelius Zeth wrote:

> Hi Tom,
>
> this doesn't help. The last 12 chains are simply thrown out in the  
> editing step.
>
> Best wishes and thank!
>
> Kornelius
>
> On Tue, 18 Dec 2007 10:15:00 -0700
>  Tom Terwilliger <terwilliger at lanl.gov> wrote:
>> Hi Kornelius,
>>
>> I am checking this out...but for the moment here is a solution:
>>
>> You can use 2-character chain codes in phenix.  They go in the usual
>> column for chain ID and the column just before it.
>>
>> So columns 21-22 in your PDB file could be:
>> " A"  (chain A, usual syntax)
>> " B"
>> " C" ...etc
>> " 0"
>> " 1"
>> " 9"
>> "AA" (chain AA, recognized only by  hybrid-36 compatible programs)
>> "AB"
>> "AC" ...etc
>>
>> -Tom T
>>
>> At 06:34 AM 12/18/2007, you wrote:
>>> Dear all,
>>>
>>> I'm trying to refine/rebuild a structure of 48 identical chains. In
>>> Refmac the small letters a, b, c and 0 1 2 for the chains work quite
>>> well and are distinguished. However that does not apply to Phenix
>>> which sees A equal to a. What might be the solution to use?
>>>
>>> Thanks and best wishes
>>>
>>> Kornelius
>>>
>>>  ----------------------------------------------
>>>  Kornelius Zeth
>>>  Max Planck Institute for Developmental Biology
>>>  Dept. Protein Evolution
>>>  Spemannstr. 35
>>>  72076 Tuebingen, Germany
>>>  kornelius.zeth at tuebingen.mpg.de
>>>  Tel -49 7071 601 323
>>>  Fax -49 7071 601 349
>>> _______________________________________________
>>> 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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>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>  ----------------------------------------------
>  Kornelius Zeth
>  Max Planck Institute for Developmental Biology
>  Dept. Protein Evolution
>  Spemannstr. 35
>  72076 Tuebingen, Germany
>  kornelius.zeth at tuebingen.mpg.de
>  Tel -49 7071 601 323
>  Fax -49 7071 601 349
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

-- 
Paul Adams
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Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

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