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

[Damian Ekiert]

Clemens,

Thanks, that makes sense.  I usually specify which data columns I am using in Refmac and Phenix, slipped my mind when I started fiddling with Buster.

I was under the impression that "-r 0.010" was the default bonds target, is that not correct?  I put it in the command file explicitly just so it would be handy if it needed to fiddle with it at some point, but perhaps I misunderstood and am changing something unintentionally?

Thanks for you help/suggestions.

Best,

Damian







On Sep 27, 2010, at 12:16 AM, Clemens Vonrhein wrote:

> 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
> giving
> 
>  % 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
>  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?
> 
> Cheers
> 
> Clemens
> 
> 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
> *--------------------------------------------------------------
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