[phenixbb] Adding H atoms - AssertionError

[Kristof Van Hecke]

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
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
> -- 
> 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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb