[bug #24131] BMRB export fails with 'SpinContainer' object has no attribute 's2'

[Martin Ballaschk]

URL:
<http://gna.org/bugs/?24131>

Summary: BMRB export fails with 'SpinContainer' object has no
attribute 's2'
Project: relax
Submitted by: mab
Submitted on: Mon 30 Nov 2015 02:37:31 PM UTC
Category: relax's source code
Specific analysis category: None
Priority: 5 - Normal
Severity: 4 - Important
Status: None
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Release: 4.0.0
Discussion Lock: Any
Operating System: Mac OS X (Intel)

_______________________________________________________

Details:

Hi Edward,

after the final run of the d'Auvergne protocol, relax writes a results.bz2
file, containing all the relaxation rates and model-free data etc of the
current run.

To export to a NMRstar file, one needs to set up spin.isotope, spin.element
(which apparently are not preserved from the original final run),
relax_data.temp_calibration, relax_data.temp_control, molecule.type and
bmrb.thiol_state.

But then, a bmrb.write(file="test.str", dir=None, version='3.1', force=True)
results in:
AttributeError: 'SpinContainer' object has no attribute 's2'

How can I setup that the s2 and the other model-free parameters are written
out into the BMRBstar file along with the relaxation data?

I can't provide a truncated results file (because I don't know how to truncate
it) and don't want to publish the results here. So the full results file is
available on request …

Cheers,
Martin



_______________________________________________________

File Attachments:


-------------------------------------------------------
Date: Mon 30 Nov 2015 02:37:31 PM UTC Name: relax_output.txt Size: 11kB
By: mab

<http://gna.org/bugs/download.php?file_id=25869>

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[Edward d Auvergne]

Update of bug #24131 (project relax):

Specific analysis category: None => Model-free analysis
Status: None => Need Info
Assigned to: None => bugman
Operating System: Mac OS X (Intel) => All systems
Summary: BMRB export fails with 'SpinContainer' object has no
attribute 's2' => BMRB export fails with 'SpinContainer' object has no
attribute 's2'.

_______________________________________________________

Follow-up Comment #1:

I would suggest using the residue.delete user function in a few tests to
narrow this down to one or two spins, then save a new results file. Using
ranges such as ":1-100" to delete residues 1 to 100 will make this a quick
process.

You could then slightly randomise the data, change the molecule name, etc. all
within the XML file using a text editor. Note, the number is really stored as
the <ieee_754_byte_array> value, but you can delete this tag if you are
careful. Or you can edit the values directly as:

cdp.mol[0].res[0].spin[0].s2
cdp.mol[0].res[0].spin[0].relax_data['R1_600']

If you could attach such a truncated and obfuscated results file, I can then
add the file to relax and create a new system test based on the current
'relax_output.txt' file to catch the bug. Cheers!

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[Martin Ballaschk]

Follow-up Comment #2, bug #24131 (project relax):

This was fast!

I attached a file ("two_spins.bz2") with two residues, residue 6 (without an
s2 parameter) and residue 7 (with an s2 parameter).

After deleting the spin with the missing value, write.bmrb went through just
fine. So I suppose the problem ist the missing value.


(file #25870, file #25871)
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Additional Item Attachment:

File name: bmrb-deposition.py Size:1 KB
File name: two_spins.bz2 Size:43 KB


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[Edward d Auvergne]

Follow-up Comment #3, bug #24131 (project relax):

I would have guessed this to be the problem, but I need to check why it is not
skipped. The system test is important to check if the bug is fixed, and that
it never returns. Cheers!

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[Edward d Auvergne]

Update of bug #24131 (project relax):

Status: Need Info => Fixed
Open/Closed: Open => Closed


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[Martin Ballaschk]

Follow-up Comment #6, bug #24131 (project relax):

The file I attached earlier contained only one spin with no relaxation data.
Whith the latest svn version, the absent spins get skipped.

Check the file spins-6-7.bz2, where really are two residues, one without and
one without data …

Now relax tells me when trying to export
"RelaxError: No interatomic interactions are defined for the spin
'#1ogt-hkca_mol2:***@N'."



(file #25872)
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Additional Item Attachment:

File name: spins-6-7.bz2 Size:100 KB


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[Martin Ballaschk]

Follow-up Comment #7, bug #24131 (project relax):

To add on my earlier comment:

When encountering a spin without data, I get the above error message about
missing interatomic interaction.

If I define interactions with:
interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)

the routine gets blocked on encountering the spin with data:
RelaxError: The magnetic dipole-dipole interaction already exists between
the spins '#1ogt-hkca_mol2:***@N' and '#1ogt-hkca_mol2:***@H'.

So either way it doesn't work and I'm stuck …

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[Edward d Auvergne]

Follow-up Comment #8, bug #24131 (project relax):

Try running 'svn up' again. After creating the system test and making it
pass, I found other system tests failing and fixed those (see comment #5
below). The behaviour should now be quite different, but I don't know if
everything is fixed, so more system tests might be necessary.

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[Martin Ballaschk]

Follow-up Comment #9, bug #24131 (project relax):

Unfortunately, it didn't pass …

Run the attached (almost identical) scripts and see if you can reproduce what
I see.

fails_missing_interaction.py –– fails because there is no interaction
defined.

fails_duplicate_interaction.py –– fails because I tried to define
interactions.

(file #25876, file #25877)
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Additional Item Attachment:

File name: fails_duplicate_interaction.py Size:1 KB
File name: fails_missing_interaction.py Size:1 KB


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[Edward d Auvergne]

Update of bug #24131 (project relax):

Status: Fixed => In Progress
Open/Closed: Closed => Open


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[Edward d Auvergne]

Follow-up Comment #12, bug #24131 (project relax):

Ok, a new fix has been committed (see comment #11 below). Could you please
check again? Note that the RelaxError from the fails_duplicate_interaction.py
script should be there, as the interatomic N-H interaction is already defined.

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[Martin Ballaschk]

Follow-up Comment #13, bug #24131 (project relax):

Looks great! Relax now wrote out the data from the whole data pipe without
complaining. And the str file looks rather complete at the first glance.

Thanks a lot for resolving this so quickly! :)

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[Edward d Auvergne]

Update of bug #24131 (project relax):

Status: In Progress => Fixed
Open/Closed: Open => Closed

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Follow-up Comment #14:

No problems - this was quite an easy and quick one to solve with the data and
scripts you attached. Cheers!

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