[buster-discuss] Rfree/Rwork gap
ClAuS Flensburg
claus at globalphasing.com
Mon Mar 7 14:16:13 CET 2016
Dear Zheng,
sorry for missing the message on buster-discuss.
On Fri, Feb 26, 2016 at 07:20:57PM +0800, Zheng Zhou wrote:
....
(snip R-Rfree question answered by Gerard on CCP4BB)
....
> A second question, if I want to define my own TLS group.
>
> Would this text file work:
> TLS DETAILS
> NUMBER OF TLS GROUPS: 6
> TLS GROUP: 1
> SET: {A|*}
> TLS GROUP: 2
> SET: {B|*}
not directly. The syntax is explained on:
https://www.globalphasing.com/buster/manual/autobuster/manual/autoBUSTER3.html#tls
so for six groups in chains A to F you can:
% cat > one-tls-per-chain.tls <<eof
NOTE BUSTER_TLS_SET tlsA { A|* }
NOTE BUSTER_TLS_SET tlsB { B|* }
NOTE BUSTER_TLS_SET tlsC { C|* }
NOTE BUSTER_TLS_SET tlsD { D|* }
NOTE BUSTER_TLS_SET tlsE { E|* }
NOTE BUSTER_TLS_SET tlsF { F|* }
eof
Use this TLS specification file the *first* time you run BUSTER:
% refine ... -TLS one-tls-per-chain.tls -d 10 >& 10.log
Since BUSTER puts all the TLS parameters in the output PDB file you can
then do:
% refine -p 10/refine.pdb ... -TLS -d 20 >& 20.log
This makes BUSTER load the TLS specifications from the 10/refine.pdb file
and switch on the refinement of the TLS parameters.
You could also use the TLSbasic macro (see "refine -M list" or
https://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterTLSintro)
% refine ... -M TLSbasic -d 11 >& 11.txt
% refine -p 11/refine.pdb ... -TLS -d 21 >& 21.txt
Hope this helps,
ClAuS, Clemens & Gerard (for buster-develop)
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