Hi Stefano,
It's no problem at all. For bugs, it is best to create a bug report
using the link http://gna.org/bugs/?func=additem&group=relax. With a
bug report, all the files required to reproduce the bug can be
attached (ideally truncated to 1-2 spins). If I can reproduce the bug
with truncated data, in most cases I can then create a system test and
have a fix within about 5 to 10 minutes.
In this case here, it looks like an improperly defined sheet secondary
structure element in the PDB. The error is the IndexError, all text
after that can be ignored. With the bug report and attached PDB file,
I can have a look and see if I can make the relax PDB reader more fail
safe. This is a constant battle due to the huge number of programs
which create corrupted PDB files! It's really not hard to follow the
PDB standard, but there are just too many lazy developers out there.
Regards,
Edward
On 18 March 2014 10:13, Stefano Luciano Ciurli <stefano.ciurli@xxxxxxxx>
wrote:
Hello,
I hope I do not bug you too often, but I keep receiving error messages.
Here is one, upon loading a PDB file generated using Chimera, and no spins
are loaded in the spin viewer. I am using 3.1.7.
Stefano
Internal relax PDB parser.
Opening the file '/Users/stefano/Desktop/13-BpUreE-NMR/Manuscript/Figure
6,7 - Dynamics/relax/dimer_H.pdb' for reading.
Traceback (most recent call last):
File "gui/interpreter.pyc", line 303, in run
File "pipe_control/structure/main.pyc", line 722, in read_pdb
File "lib/structure/internal/object.pyc", line 1813, in load_pdb
File "lib/structure/internal/object.pyc", line 500, in _parse_pdb_ss
File "lib/structure/pdb_read.pyc", line 1221, in sheet
IndexError: string index out of range
Exception in thread Thread-1:
Traceback (most recent call last):
File "threading.pyc", line 808, in __bootstrap_inner
File "gui/interpreter.pyc", line 323, in run
File "status.pyc", line 369, in release
File "status.pyc", line 413, in notify
File "gui/analyses/auto_model_free.pyc", line 276, in activate
File
"/Applications/relax.app/Contents/Resources/lib/python2.7/wx/_core.py",
line 16769, in CallAfter
AssertionError: callableObj is not callable
Re: Error message upon PDB loading