[buster-discuss] defining solvent content - missing part of structure

[Clemens Vonrhein]

Dear Michael,

before you spend additional time with some out-of-date documentation
and tools, a quick initial reply ...

On Tue, May 07, 2013 at 09:59:18AM +0200, Michael Hothorn wrote:
> I am trying to refine a partial model: I have a molecular
> replacement solution that comprises about 50% of the asymmetric unit
> and I would like to specify the scattering mass that is missing in
> the initial pdb file to buster.

Yes, that seems a good idea.

> I read in the manual that this can be done by supplying
> a TNT sequence file
>
> $BDG_home/bin/buster/pirToSeq.pl <file.pir>
>                     <file.seq>

These are very old pages from the time BUSTER was still run through
the BUFFET gui (and unfortunately still coming up high in google). For
the BUSTER versions since 2009, the main source of documentation is
the BUSTER wiki at

  http://www.globalphasing.com/buster/wiki/

with a lot of examples and tutorials ... unfortunately not about the
'missing atom channel' (we need to add this).

> However, I cannot find the recommended script in my buster 2.10
> installation:

That is correct. If you could find it it would mean that you are
probably running a very old production version of BUSTER.

> Could you please provide advice on how to specify the missing atoms
> to buster (so that it assumes the correct solvent content for
> example).

Have a look at the MissingAtoms macro (see 'refine -M list' for a
list and explanation of available macros). If you have 100
residues missing (assuming 11 atoms per residue) you could be
using something like

  refine -p your.pdb -m your.mtz -autoncs \
         -M MissingAtoms nmiss=1100 ... -d 01 | tee 01.lis

Make sure you compare the reciprocal-space CC plots with and without
this missing-channel option:

  http://www.globalphasing.com/buster/wiki/index.cgi?BusterCCplot

Don't worry about the solvent content: this is reported only for your
information (but internally not used in this scenario).

Hope that helps.

Cheers

Clemens (for buster-develop)

-- 

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