bugrelax - Bugs: bug #21187, "NoneType" error message...

 
 
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bug #21187: "NoneType" error message while loading side chain amide protons

Submitted by:  Martin Ballaschk <mab>
Submitted on:  Thu 10 Oct 2013 10:17:18 AM UTC  
 
Category: relax's source codeSpecific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: Repository: trunkOperating System: All systems

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(Jump to the original submission Jump to the original submission)

Thu 10 Oct 2013 12:55:05 PM UTC, comment #12:

For more discussions, see the mailing list thread at http://thread.gmane.org/gmane.science.nmr.relax.devel/4654.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 10 Oct 2013 12:42:22 PM UTC, comment #11:

Thank you for the workaround! Is this fix already in the SVN now?

It's a shame that AMBERs "reduce" generates faulty files. I actually liked using it because it makes a few little adjustments after adding the hydrogens. But if this gives me de facto corrupted files I maybe just should use the attach_protons function of relax!

Probably the conformational differences are too small to make a real difference in the subsequent MF analysis, given how large the actual errors of my rates etc actually are. I will look into this and if there's any difference, report back here.

Martin Ballaschk <mab>
Thu 10 Oct 2013 12:22:36 PM UTC, SVN revision 21052:

Merged revisions 21051 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r21051 | bugman | 2013-10-10 14:21:49 +0200 (Thu, 10 Oct 2013) | 9 lines

Fix for bug #21187 - the corrupted PDB issue with protons atom numbers of zero.

The bug at https://gna.org/bugs/?21187 was reported by Martin Ballaschk (https://gna.org/users/mab).

The fix was to allow for spin containers in the relax data store to have the same atom number, as
long as the atom names are different. Note - this may cause problems in the future so a better
solution might have to be found.
........

(Browse SVN revision 21052)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 10 Oct 2013 12:21:49 PM UTC, SVN revision 21051:

Fix for bug #21187 - the corrupted PDB issue with protons atom numbers of zero.

The bug at https://gna.org/bugs/?21187 was reported by Martin Ballaschk (https://gna.org/users/mab).

The fix was to allow for spin containers in the relax data store to have the same atom number, as
long as the atom names are different. Note - this may cause problems in the future so a better
solution might have to be found.

(Browse SVN revision 21051)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 10 Oct 2013 12:05:25 PM UTC, comment #8:

Many programs produce corrupted PDB files. I don't understand why, it's really incredibly easy to abide by the PDB standard when writing out a file - as relax does. I think I have a solution ready for you anyway.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 10 Oct 2013 12:02:13 PM UTC, comment #7:

I see, that PDB is just the output I got from AMBER's reduce function. I will look into this.

Martin Ballaschk <mab>
Thu 10 Oct 2013 11:59:33 AM UTC, SVN revision 21050:

Merged revisions 21049 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r21049 | bugman | 2013-10-10 13:58:50 +0200 (Thu, 10 Oct 2013) | 5 lines

Created the Structure.test_bug_21187_corrupted_pdb system test to catch bug #21187.

The bug at https://gna.org/bugs/?21187 was reported by Martin Ballaschk (https://gna.org/users/mab).
........

(Browse SVN revision 21050)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 10 Oct 2013 11:58:50 AM UTC, SVN revision 21049:

Created the Structure.test_bug_21187_corrupted_pdb system test to catch bug #21187.

The bug at https://gna.org/bugs/?21187 was reported by Martin Ballaschk (https://gna.org/users/mab).

(Browse SVN revision 21049)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 10 Oct 2013 11:52:56 AM UTC, comment #4:

Ha, just realized you asked for 5 lines, I understood you want 5 residues. See the new minimal file attached.

(file #19148)

Martin Ballaschk <mab>
Thu 10 Oct 2013 11:51:08 AM UTC, comment #3:

The problem is due to a corrupted PDB file. Atom numbers (the second column) must be sequential. The numbers of 0 are invalid according to the PDB standard. I will nevertheless see if there is a solution. If not, I can throw a RelaxError to indicate that this is a fatal PDB corruption - this will be much more informative that the missing 'pos' variable error.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 10 Oct 2013 11:42:53 AM UTC, comment #2:

Ok, I attached "molecule.pdb" that gives me the described error.

(file #19147)

Martin Ballaschk <mab>
Thu 10 Oct 2013 10:24:23 AM UTC, comment #1:

Could you attach to this bug report a truncated PDB file (with a maximum of ~5 lines) which shows this problem along with a relax script which loads the file and shows the problem? That should allow me to fix the problem within 5 minutes. Cheers!

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 10 Oct 2013 10:17:18 AM UTC, original submission:

First, set up you data pipe and read a pdb with already-attached protons (with Trp residues).

pipe.create("example", 'mf')
structure.read_pdb('molecule.pdb', set_mol_name='my_molecule')

Loading backbone N and H works, as well as NE1:
structure.load_spins('@N', ave_pos=True)
structure.load_spins('@NE1', ave_pos=True)
structure.load_spins('@H', ave_pos=True)

But loading the side chain amide proton fails:

relax> structure.load_spins('@HE1', ave_pos=True)
Adding the following spins to the relax data store.

Traceback (most recent call last):
File "<console>", line 1, in <module>
File "/usr/local/Cellar/relax/3.0.0/prompt/uf_objects.py", line 221, in _call_
self._backend(*new_args, **uf_kargs)
File "/usr/local/Cellar/relax/3.0.0/pipe_control/structure/main.py", line 608, in load_spins
spin_cont.pos = pos
AttributeError: 'NoneType' object has no attribute 'pos'

Martin Ballaschk <mab>

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

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Attached Files
file #19148:  molecule1.pdb added by mab (332B - chemical/x-pdb)
file #19147:  molecule.pdb added by mab (5kB - chemical/x-pdb)

 

Depends on the following items: None found

Items that depend on this one: None found

 

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    Follow 10 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Thu 10 Oct 2013 12:23:04 PM UTCbugmanStatusIn Progress=>Fixed
      Open/ClosedOpen=>Closed
    Thu 10 Oct 2013 12:05:25 PM UTCbugmanStatusConfirmed=>In Progress
    Thu 10 Oct 2013 11:52:56 AM UTCmabAttached File-=>Added molecule1.pdb, #19148
    Thu 10 Oct 2013 11:51:33 AM UTCbugmanRelease3.0.0=>Repository: trunk
      Operating SystemNone=>All systems
    Thu 10 Oct 2013 11:47:05 AM UTCbugmanStatusNeed Info=>Confirmed
    Thu 10 Oct 2013 11:42:53 AM UTCmabAttached File-=>Added molecule.pdb, #19147
    Thu 10 Oct 2013 10:24:23 AM UTCbugmanStatusNone=>Need Info
      Assigned toNone=>bugman
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