[buster-discuss] AutoBuster refine - permissions problem

[Claus Flensburg]

Hi Antony,

On Wed, Oct 24, 2012 at 06:31:17PM +0000, Antony Oliver wrote:
> Thank you Nicholas - 
> 
> I have indeed used the -d option to use a directory (BUSTER1) that I have full read/write/execute permissions for - hence my question! Completely confused....

yeah, looks like it's the "copy='cp -p'" part that tries to change ownership:

> >> cp: chown: BUSTER1/01-BUSTER/Cycle-1/restraint_dictionaries/SO4.cif: Permission denied
         ^^^^^
> >> 
> >>  ESC[1mERRORESC[m : [pdb2tnt-0022] unable to save a copy of
> >>          /usr/local/buster/tnt/data/common-compounds/SO4.cif
> >>          into
> >>          BUSTER1/01-BUSTER/Cycle-1/restraint_dictionaries/SO4.cif

you might be able to get around it by doing:

===
/bin/bash
. /usr/local/buster/setup.sh
copy=/bin/cp refine -m file.mtz -p file.pdb ... -d buster2
===

Does this work for you?


Regards,

ClAuS (for buster-develop)


> 
> Antony.  
> 
> Sent from my iPhone
> 
> On 24 Oct 2012, at 19:27, "Nicolas Foos" <Nicolas.Foos at afmb.univ-mrs.fr> wrote:
> 
> > Dear Antony,
> > 
> > maybe it's mistake, but have you try to define the directory where 
> > buster write files. More precisely, have you use the -d option ?
> > I think that it's the place where you write your destination file which 
> > cause your problem.
> > 
> > Hope to help you.
> > 
> > Nicolas
> > 
> > 
> > Le 24/10/12 17:57, Antony Oliver a écrit :
> >> I am having a little bit of a problem running refine which I can't seem to resolve - see snips from the relevant log files below?
> >> Could someone help and shine some light on the possible issue?
> >> 
> >> There is obviously a permissions error - but where?!!!  It all looks okay.
> >> 
> >> NB: Running on OS X / darwin.
> >> 
> >> With thanks,
> >> 
> >> Antony.
> >> 
> >> 
> >> 
> >> 
> >> 
> >> <snip1 >
> >> 
> >>>>> ab_pdb2tnt >>>
> >>>>> ab_pdb2tnt >>> Extracted from file BUSTER1/01-BUSTER/Cycle-1/ab_pdb2tnt.log :
> >>>>> ab_pdb2tnt >>>
> >>>>> ab_pdb2tnt >>> ERROR : [pdb2tnt-0022] unable to save a copy of
> >>>>> ab_pdb2tnt >>>         /usr/local/buster/tnt/data/common-compounds/SO4.cif
> >>>>> ab_pdb2tnt >>>         into
> >>>>> ab_pdb2tnt >>>         BUSTER1/01-BUSTER/Cycle-1/restraint_dictionaries/SO4.cif
> >>>>> ab_pdb2tnt >>>
> >> 
> >>  ERROR : [run_buster-0032] problems in ab_pdb2tnt - see
> >>          above and BUSTER1/01-BUSTER/Cycle-1/ab_pdb2tnt.log
> >> 
> >> 
> >>  ERROR : [refine-0057] problems in run_buster: see messages
> >>          above
> >> 
> >> </snip 1>
> >> 
> >> 
> >> <snip 2>
> >> 
> >>  ###################### 4. processing missing restraints ######################
> >> 
> >> cp: chown: BUSTER1/01-BUSTER/Cycle-1/restraint_dictionaries/SO4.cif: Permission denied
> >> 
> >>  ESC[1mERRORESC[m : [pdb2tnt-0022] unable to save a copy of
> >>          /usr/local/buster/tnt/data/common-compounds/SO4.cif
> >>          into
> >>          BUSTER1/01-BUSTER/Cycle-1/restraint_dictionaries/SO4.cif
> >> 
> >> </snip 2>
> >> 
> >> 
> >> 
> >> ---
> >> Dr Antony W Oliver
> >> Senior Research Fellow
> >> CR-UK DNA Repair Enzymes Group
> >> Genome Damage and Stability Centre
> >> Science Park Road
> >> University of Sussex
> >> Falmer, Brighton, BN1 9RQ
> >> 
> >> email: antony.oliver at sussex.ac.uk
> >> tel (office): +44 (0)1273 678349
> >> tel (lab): +44 (0)1273 677512
> >> 
> >> _______________________________________________
> >> buster-discuss mailing list
> >> buster-discuss at globalphasing.com
> >> https://www.globalphasing.com/mailman/listinfo/buster-discuss
> > 
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