[buster-discuss] [EXTERNAL] Re: Documentation on some commandline options for refine

Mon Oct 13 11:05:39 CEST 2025

Hi Clemens,

Thanks for your helpful reply. I think that knowing how to assign ncs relations in details to buster satisfies our needs as we want to sometimes use different refinement programs but with the same input parameters and ncs relations.

On a different note, I am also working on supplying a water addition program to buster refine which we have developed in house. Currently we supply the commandline arguments
-WAT WaterUpdateProgram=<water_addition_exec_path>
to buster refine. From https://www.globalphasing.com/buster/manual/autobuster/manual/water_updater.sh
I understand that the water update program takes posiional arguments in the order:

pdb=$1                            # current PDB file
mtz_2=$2                          # MTZ-file for 2Fo-Fc map (columns 2FOFCWT/PH2FOFCWT)
mtz_1=$3                          # MTZ-file for  Fo-Fc map (columns FOFCWT/PHFOFCWT)
subdir=$4                         # [sub-]directory for this run (e.g. for writing additional
                                                          # output to - uniquely named!)
out=$5                            # name of output PDB file (should be a copy of the input PDB
                                                        # file as much as possible, with only the waters updated)

But when I with another water addition program using the same positional arguments the refinement stops with an error message likely due to a bug I have introduced in my water addition program. My problem is that there's no output to stdout or stderr indicating what is wrong (unlike when running the water addition program standalone). Is it possible to set an option in Buster refine to emit stderr to the console so I can better debug the problem? Maybe there's a log file somewhere with this error output?

Finally, I would like to know if buster refine has an option for occupancy refinement of part of the molecule or ligands to be refined.

Many thanks,

Robert

-----Original Message-----
From: Clemens Vonrhein <vonrhein at globalphasing.com>
Sent: 03 October 2025 15:06
To: Robert Oeffner <robert.oeffner at astx.com>
Cc: BUSTER Developers <buster-discuss at globalphasing.com>
Subject: Re: [buster-discuss] [EXTERNAL] Re: Documentation on some commandline options for refine

Hi Robert,

as a small addition: BUSTER (and the interfaces "refine" and
"aB_autorefine") changes permanently - so it could be a good idea to review the need and logic behind some existing arguments and settings when moving from one (older) system to another (newer) one.

We would always recommend using "aB_autorefine" as a starting point for refinement if you want to see what some simple defaults could do. Changing some individual restraint weights might have the desired effect, but could alter e.g. the automatic X-Ray weight adjustment if not handled carefully.

Anyway, just to say: if users feel the need to move away from running BUSTER with (basically) all defaults, we would definitely like to hear about the exact reasons, effects and specific conditions: it would help us to see where BUSTER and/or documentation could be improved :-)

Cheers

Clemens

On Tue, Sep 23, 2025 at 12:45:58PM +0000, Robert Oeffner via buster-discuss wrote:
> Thank you.
>
> Robert
>
> -----Original Message-----
> From: BUSTER Developers <buster-discuss at globalphasing.com>
> Sent: 23 September 2025 12:10
> To: Robert Oeffner <robert.oeffner at astx.com>
> Cc: buster-discuss at globalphasing.com
> Subject: [EXTERNAL] Re: [buster-discuss] Documentation on some
> commandline options for refine
>
> Dear Robert,
>
> On Tue, Sep 23, 2025 at 10:51:49AM +0000, Robert Oeffner via buster-discuss wrote:
> > Dear Buster developers,
> >
> > At my work I am porting an in-house wrapper script for buster into a python script. To that end I am reading up on some of the command line options that we use. But I fail to find documentation for some of the options such as "wtors=<float>", "-n <int>" and "-N <int>", which is part of the commandline options that we supply to the refine program. I guess the above options are torsion restrant weight, nsmall and nbig although I am not sure.
> >
> > Would you be able to point me to documentation about this? I have
> > been looking at BUSTER Documentation :
> > Usage<https://www.globalphasing.com/buster/manual/autobuster/manual/
> > au toBUSTER4.html#refine_args_r> BUSTER Documentation : Appendix
> > 1<https://www.globalphasing.com/buster/manual/autobuster/manual/appe
> > nd
> > ix1.html> DocumentationTopPage -
> > Kwiki<https://www.globalphasing.com/buster/wiki/index.cgi?Documentat
> > io
> > nTopPage>
> > but to no avail.
> >
> > Many thanks,
> >
> > Robert
>
> The wtors variable refers to the (relative) weight for the torsion terms in the geometry part of the total function that is being optimised. It is the same as GeometryWeight_torsion (see [1] and [2]).
> As you can see the default is 2.0. It is rarely changed.
>
>
> Hope this helps,
>
> ClAuS (for BUSTER Developers)
>
> [1] Section 3 of
> https://www.globalphasing.com/buster/manual/autobuster/manual/autoBUST
> ER6.html#parameters [2]
> https://www.globalphasing.com/buster/manual/autobuster/manual/appendix
> 1.html#SetvarParameter_GeometryWeight_torsion
>
>
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>
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--

*--------------------------------------------------------------
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., 9 Journey Campus, Castle Park
* Cambridge CB3 0AX, UK                   www.globalphasing.com
*--------------------------------------------------------------

This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.