[buster-discuss] target restraints definition in buster

Clemens Vonrhein vonrhein at globalphasing.com
Thu Jul 14 20:41:32 CEST 2016

Dear Michael,

On Wed, Jul 13, 2016 at 09:25:34AM +0200, Michael Hothorn wrote:
> I am trying to refine a structure containing two individual domains
> at moderate resolution (3.4 A). Autobuster version is 2.10.3.


> I
> would like to try using external restrains using the -target switch.

Good idea ...

> I have high resolution structures of both domains (100% sequence
> identity, some conformational changes in one of the domains).

... especially given that you have those high-res structures.

> My questions:
> 1. how do I define the two different domains: Should they be
> provided in one or two separate .pdb files, calling the -target
> switch twice?

The easiest would be to provide a single PDB file: just superimpose
the high-res structures onto your current low-res model, i.e.

  HighRes-dom1 --> dom1
  HighRes-dom2 --> dom2

This can easily be done in Coot for example. Then combine (merge) the
two placed high-res structures into a single PDB file.

After that use

  refine -target HighRes_dom1-dom2.pdb -m lowres.pdb -p lowres.mtz ...

Of course, if you solved your structure by placing the two high-res
structures using molecular replacement, then you could just use your
initial MR model as PDB file for LSSR targeting.

> 2. do they need to have different chain IDs?

They need to match the chain ID and residue numbering of your current
low-res model so that residue A12 in HighRes_dom1-dom2.pdb and A12 in
lowres.pdb are the same residue.

> 3. where can I find information about the mapping of the external
> restraints to the structure being refined (which logfile to look at
> during the run)?

That would be the LIST.html file (location reported on stdout): search
for string "target" in there. However, you might find the information
in there more geared towards developers - what type of information are
you looking for exactly?




* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK                   www.globalphasing.com

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