[buster-discuss] Rfree/Rwork gap

Zheng Zhou zhengzhouzz at gmail.com
Thu Mar 10 08:45:01 CET 2016


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)


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