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

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" 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 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb