[phenixbb] chain definition in phenix

Kornelius Zeth kornelius.zeth at tuebingen.mpg.de
Tue Dec 18 11:26:57 PST 2007


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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 ----------------------------------------------
 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



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