[buster-discuss] 01-BUSTER vs 02-BUSTER?

Clemens Vonrhein vonrhein at globalphasing.com
Mon Sep 27 09:16:49 CEST 2010

Hi Damian,

these two subdirectories are due to the fact that you have two sets of
amplitude/sigma in your MTZ file. BUSTER will refine against all
sF/SIGF-type pairs - or more accurately: every pair of type amplitude
(F) and sigma (Q). You can set which F/Q pairs should be used by

  % refine autoBUSTER_fss="Fnat,SIGFnat" ...

Using more than one F/Q pair happens most of the time because you are
re-using a MTZ file that comes as output from another refinement or MR
program: those steps sometimes write out modified amplitudes/sigma
columns (e.g. with anisotropy correction applied or with some scaling
or resolution cut). Here it seesm you are using the output file from
PHASER to refine against - which usually includes the original data
(or is that also scaled?) and a version with anisotropic overall
scaling, right?

I would recommend to always use your 'master' MTZ file in refinement,
since it is very easy to daisy-chain MTZ files where one never can be
sure what happened to the actually measured data. So if you use the
MTZ file just after truncate (or ctruncate) - including the test-set
flag FreeR_flag or FREE - you will be on the safe side. And you will
be getting only one subdirectory 01-BUSTER.

Two small comments about your command: you shouldn't need setting of
"-r 0.010" since the default weighting scheme usually comes up with a
good set of X_ray weights anyway. Also, a resolution cut at that stage
(with -R flag) is probably not necessary, since all resolution
decisions (beamstop masking and high-resolution cut) have been done
already during data processing and scaling/merging.

Finally, I would highly recommend saving the standard output into a
file, e.g. with

 - for tcsh/csh:

    refine -p some.pdb -m other.mtz ... -d 01 >& 01.lis 

 - for sh/ksh/bash/zsh:

    refine -p some.pdb -m other.mtz ... -d 01 2>&1

The standard output contains the most important information and can
help figuring out what is going one. Near the top it will tell you
which amplitude/sigma pairs where used.

Does that make sense?



On Sun, Sep 26, 2010 at 04:52:50PM -0700, Damian Ekiert wrote:
> Hello,
> I am trying to refine a structure in Buster for the first time and I am a bit confused about the output.  The output directory contains two subdirectories called 01-BUSTER and 02-BUSTER, which I initially thought were derived from two sequential parts of the refinement process.  But sometimes "refine.log" in linked to a file from 01-BUSTER and other times to 02-BUSTER.  Similarly, sometimes the refine.pdb coordinates are identical to 01-BUSTER/Cycle-5/BUSTER.pdb but other times 02-BUSTER/Cycle-5/BUSTER.pdb.
> Could someone please explain what is going on?  Does Buster try two different refinement strategies and pick "the best" (if so, what is different and how does it decide)?
> If this is in the documentation, I would appreciate it if someone could direct me to the correct web page, but I couldn't find anything yet.
> In case it is relevant, my command file is pasted below.
> Thanks!
> Damian Ekiert
> #! /bin/csh -f 
> refine \
> -p ../buster3/refine-coot-13_buster-in.pdb \
> -m ../phaser_1cp_dex593.mtz \
> -M TLSalternate \
> -TLS dex865_TLS.in \
> -r 0.010 \
> #-autoncs \
> #-WAT \
> -R 50 1.65
> _______________________________________________
> 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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