[phenixbb] Adding H atoms - AssertionError
Kristof Van Hecke
kristofrg.vanhecke at gmail.com
Wed Sep 5 04:58:31 PDT 2012
I've installed the latest nightly 'phenix-dev-1148', but now I get the
"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.
On 04 Sep 2012, at 19:32, Nigel Moriarty wrote:
> 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.
> On Mon, Sep 3, 2012 at 7:47 PM, Pavel Afonine <pafonine at lbl.gov>
>> 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)
>> the error occurred.
>> On 9/3/12 5:26 AM, Kristof Van Hecke wrote:
>>> When I try to add H-atoms to a metal-coordination complex (not a
>>> nor DNA) during refinement or via the ReadySet module, I get the
>>> (I have a proper restraints .cif file and without the 'add H-
>>> atoms' option
>>> during refinement, things work fine,. )
>>> AssertionError :
>>> line 233, in run
>>> return_value = self._target(self._args, self._kwargs, self._c)
>>> line 80, in __call__
>>> result = self.target()
>>> line 17, in __call__
>>> return self.target(args=list(self.args))
>>> line 1038, in run
>>> line 151, in run
>>> assert 0
>>> I have the latest version of Phenix (1.8.1069) and run it on a Mac
>>> pro (Leopard 10.5.8).
>>> Any suggestions please..?
>>> Thank you very much
>>> Kristof Van Hecke
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> 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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