Re: Error message upon PDB loading
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=additemgroup=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.ciu...@unibo.it 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 ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
Re: Error message upon PDB loading
Dear Stefano. You are really not bugging anyone with your questions! It is a welcome to see the interest in relax, and if you are becoming interested and a power user, the knowledge of relax is spread. :-) But for being able to help you, please dont hesitate to make a bug report. https://gna.org/bugs/?func=additemgroup=relax Here you can make a small description and upload the pdb file. It is necessary to use this tracker to add files, since the mailing list is not possible. And fixing your problem, could be a good reference in the future, if another user have the same problem. Best Troels 2014-03-18 10:13 GMT+01:00 Stefano Luciano Ciurli stefano.ciu...@unibo.it: 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 ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
Re: Error message upon PDB loading
Hello, But for being able to help you, please dont hesitate to make a bug report. https://gna.org/bugs/?func=additemgroup=relax done. Thanks! Stefano ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
