[buster-discuss] Rfree/Rwork gap

[Clemens Vonrhein]

Dear Zheng,

you could try the Grade webservice at

  http://grade.globalphasing.org/

where all necessary software is installed. Running with -nomogul
because you don't have a local CCDC installation is not ideal.

Cheers

Clemens

On Thu, Mar 10, 2016 at 03:45:01PM +0800, Zheng Zhou wrote:
> Dear Buster experts,
> 
> I may figure out what was the problem: the restraints from
> phenix.elbow may not be optimal. From CCP4 board, I got a suggestion
> to try grade. I met two errors.
> 
> For mogul, I could use -nomogul to disable it.
> 
> For obabel, how do I set $BDG_TOOL_OBABEL to none? I checked printenv,
> do not see this variable.
> 
> Thanks,
> 
> Zheng
> 
> On Mon, Mar 7, 2016 at 9:16 PM, ClAuS Flensburg <claus at globalphasing.com> wrote:
> > 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)
> _______________________________________________
> buster-discuss mailing list
> buster-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/buster-discuss

-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
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