[buster-discuss] AutoBuster refine - permissions problem

[Antony Oliver]

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....

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
>> 
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