[phenixbb] Adding H atoms - AssertionError - "You may not use the PHENIX installation itself as an output directory" msg

[Rafael Lemos Miguez Counago]

Hi,

I had the same issue when I moved from the point-and-click to the command
line installer (dev-1145 I think).  I installed the command line installer
in the Applications directory and when I ran phenix.refine from the gui I
got the same error message.  I then re-installed it at root and it is
working fine since. But you will need to sudo the installation.

Cheers,

Rafael.



On 5/09/12 9:58 PM, "Kristof Van Hecke" <kristofrg.vanhecke at gmail.com>
wrote:

> Dear Nigel,
> 
> I've installed the latest nightly 'phenix-dev-1148', but now I get the
> following error:
> 
> "You may not use the PHENIX installation itself as an output directory"
> 
> I definitely did not install phenix in my data directory (it's
> installed under /Applications, as all my previous version of phenix).
> Changing the data directory name or trying to create a new project
> pointing to a different directory, does not work,.
> 
> Did I overlook some environment setting here..?
> 
> 
> Thank you very much for all the kind help already.
> 
> Regards
> 
> Kristof
> 
> On 04 Sep 2012, at 19:32, Nigel Moriarty wrote:
> 
>> Kristof
>> 
>> This bug has been fixed. This is the joining of the restraints files
>> together so you should have the files on disk and you can provide them
>> all to phenix.refine.
>> 
>> Please update to a nightly or wait for the next major release in a
>> week or two.
>> 
>> Cheers
>> 
>> Nigel
>> 
>> On Mon, Sep 3, 2012 at 7:47 PM, Pavel Afonine <pafonine at lbl.gov>
>> wrote:
>>> Hi Kristof,
>>> 
>>> if Nigel haven't contacted you off list yet, could you please send
>>> us inputs
>>> necessary to reproduce this problem (in this case I guess this is
>>> your PDB
>>> file)? Also, it would be helpful if you tell what you did (clicked)
>>> before
>>> the error occurred.
>>> 
>>> Pavel
>>> 
>>> 
>>> On 9/3/12 5:26 AM, Kristof Van Hecke wrote:
>>>> 
>>>> Dear,
>>>> 
>>>> When I try to add H-atoms to a metal-coordination complex (not a
>>>> protein,
>>>> nor DNA) during refinement or via the ReadySet module, I get the
>>>> following
>>>> error:
>>>> (I have a proper restraints .cif file and without the 'add H-
>>>> atoms' option
>>>> during refinement, things work fine,. )
>>>> 
>>>> ----------------
>>>> AssertionError :
>>>> Traceback:
>>>>  File
>>>> "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/
>>>> cctbx_project/libtbx/thread_utils.py",
>>>> line 233, in run
>>>>    return_value = self._target(self._args, self._kwargs, self._c)
>>>> 
>>>>  File
>>>> "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/
>>>> cctbx_project/libtbx/runtime_utils.py",
>>>> line 80, in __call__
>>>>    result = self.target()
>>>> 
>>>>  File
>>>> "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/phenix/
>>>> wxGUI2/SimpleApp.py",
>>>> line 17, in __call__
>>>>    return self.target(args=list(self.args))
>>>> 
>>>>  File
>>>> "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/elbow/
>>>> elbow/command_line/ready_set.py",
>>>> line 1038, in run
>>>>    no_file_access=True,
>>>> 
>>>>  File
>>>> "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/elbow/
>>>> elbow/command_line/join_cif_files.py",
>>>> line 151, in run
>>>>    assert 0
>>>> -----------------
>>>> 
>>>> 
>>>> I have the latest version of Phenix (1.8.1069) and run it on a Mac
>>>> Book
>>>> pro (Leopard 10.5.8).
>>>> 
>>>> 
>>>> Any suggestions please..?
>>>> 
>>>> 
>>>> Thank you very much
>>>> 
>>>> Kristof Van Hecke
>>>> 
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> 
>>> 
>>> _______________________________________________
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>> 
>> 
>> 
>> -- 
>> Nigel W. Moriarty
>> Building 64R0246B, Physical Biosciences Division
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
>> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>> _______________________________________________
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>> http://phenix-online.org/mailman/listinfo/phenixbb
> 
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