[phenixbb] phenix.autobuild opinion on sequence file

Tom Terwilliger terwilliger at lanl.gov
Thu Nov 8 17:48:36 PST 2007

Hi Bryan,

I haven't tried your approach, but my guess would be that the correct 
sequence file will be the better way to go... The side chains are 
fitted after building main-chain so the sequence is not going to 
affect the main-chain build in any direct way (though the sequence 
will help the wizard in identifying and correcting places where loops 
are built with the wrong number of residues).

-Tom T

At 01:32 PM 11/8/2007, you wrote:
>i was thinking about giving phenix.autobuild a poly-Ser/Gly,Ala-intact (or
>other incomplete variant) _sequence_file_, so it doesn't inter alia put
>arginine into strands... though the solvent content will be imprecise..
>has anyone noticed if such a trick was more/less favorable to the (proper)
>complete sequence approach?  any pertinent detail or criticisms
>phenixbb mailing list
>phenixbb at phenix-online.org

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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