[buster-discuss] AutoBuster refine - permissions problem

[Claus Flensburg]

Dear Antony,

On Thu, Oct 25, 2012 at 09:21:02AM +0000, Antony Oliver wrote:
> Dear Claus,
> 
> That indeed works perfectly - many thanks - is there some way this can be patched / aliased in the setup file, or will I have to remember to do this in future?

you can add it to your own settings:

% echo "copy=/bin/cp" >> ~/.autoBUSTER

or make it installation wide with:

% echo "copy=/bin/cp" >> $BDG_home/opsys/Darwin.local
% echo "export copy"  >> $BDG_home/opsys/Darwin.local

The former will survive past updates.


Regards,

ClAuS (for buster-develop)



> 
> Antony.
> 
> ---
> 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
> 
> On Oct 24, 2012, at 7:56 PM, Claus Flensburg wrote:
> 
> > 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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