[buster-discuss] AutoBuster refine - permissions problem

[Antony Oliver]

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?

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
>>>> 
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