[phenixbb] Adding H atoms - AssertionError

[Nigel Moriarty]

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
>>
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>> 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