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

[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_mol2:7@N' and '#1ogt-hkca_mol2:7@H'.

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

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

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

[Edward d Auvergne]

Update of bug #24131 (project relax):

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


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

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

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

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

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

[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_mol2:6@N'." 



(file #25872)
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Additional Item Attachment:

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


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

[Edward d Auvergne]

Update of bug #24131 (project relax):

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


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

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

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

[Martin Ballaschk]

URL:
  

 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)

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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



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File Attachments:


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



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

[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'.

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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  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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