[buster-discuss] ERROR : [run_buster-0006] unknown argument

[Clemens Vonrhein]

Hi Wolfram,

that command is incorrect because the resolution limit is given as a
single number (when it needs a low and high-res limimt). The more
interesting command to show would be your actual 'refine'
command-line.

What is a bit surprising is that if there is an error with the
'refine' command, BUSTER should already stop early with a (hopefully)
meaningful message at this point. Could you check your 'refine ...'
command again and/or send it to us - so we can see if there is a
particular syntax and/or ordering that we haven't anticipated yet for
error checking.

Cheers

Clemens

PS: any reason for running grouped B-factor refinement at 1.9A
    resolution (if I interpret that correctly)?


On Fri, Jul 19, 2019 at 04:54:20PM -0400, wtempel wrote:
> Hi all,
> on a newly installed
> Version: 2.10.3 <2019-06-07 02:20:06>
> on
> 4.15.0-54-generic #58-Ubuntu SMP Mon Jun 24 10:55:24 UTC 2019 x86_64 x86_64
> x86_64 GNU/Linux
> a refine run fails with:
> 
> /usr/local/xtal/buster-2019-07-19/autoBUSTER/bin/linux64/run_buster
> ColumnName_FreeR_flag=FreeR_flag -noMaxEnt -n 0 -c 100 RunHarvest=yes
> -B group-mcsc -R 1.9 -Seq /home/user1/data/pXYZ/0717/buster/TNT1.seq
> -g /tmp/user1-1563557695-refine*13159.elib -p
> /tmp/user1-1563557695-refine*13159.pdb.1 -m run4/mtzchk.mtz -f F -s
> SIGF -w 4.0 -d run4/01-BUSTER/Cycle-1
>  ERROR : [run_buster-0006] unknown argument
>          “/home/user1/data/pXYZ/0717/buster/TNT1.seq”
>  ERROR : [refine-0060] problems in run_buster: see messages
>          above
> 
> 
> Leaving out the -Seq parameter produces a different error:
> 
>     /usr/local/xtal/buster-2019-07-19/autoBUSTER/bin/linux64/run_buster
> ColumnName_FreeR_flag=FreeR_flag -noMaxEnt -n 0 -c 100 RunHarvest=yes
> -B group-mcsc -R 1.9 -g /tmp/user1-1563557366-refine*2231.elib -p
> /tmp/user1-1563557366-refine*2231.pdb.1 -m run3/mtzchk.mtz -f F -s
> SIGF -w 4.0 -d run3/01-BUSTER/Cycle-1
>  ERROR : [run_buster-0006] unknown argument
>          “/tmp/user1-1563557366-refine__2231.elib”
>  ERROR : [refine-0060] problems in run_buster: see messages
>          above
> 
> 
> Any ideas what might be the problem (or a solution)?
> Thank you.
> Wolfram Tempel

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-- 

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