URL:
<http://gna.org/bugs/?19982>
Summary: dipole_pair.set_dist throws crypric error message
Project: relax
Submitted by: mab
Submitted on: Wed 25 Jul 2012 01:21:12 PM GMT
Category: GUI
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: 2.1.0
Operating System: Mac OS X (Intel)
_______________________________________________________
Details:
I tried using relaxGUI without providing structure data, for local_tm and
sperical diffusion models. While trying to setup the NH distance, something
strange happened:
dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02e-10)
Traceback (most recent call last):
File "gui/interpreter.pyc", line 299, in run
File "generic_fns/dipole_pair.pyc", line 237, in set_dist
File "generic_fns/interatomic.pyc", line 234, in interatomic_loop
KeyError: '#1shg-H_mol1:7@N'
Here's what I set up:
1. Read @N spins from a relaxation output file, via the spin editor, works
nicely:
relax> sequence.read(file='rx_t1.out', dir=None, spin_id_col=None,
mol_name_col=None, res_num_col=2, res_name_col=3, spin_num_col=None,
spin_name_col=5, sep=None, spin_id=None)
Opening the file 'rx_t1.out' for reading.
# mol_name res_num res_name spin_num spin_name
None 6 LYS None N
.
.
.
2. Attach protons:
relax> sequence.attach_protons()
3. Set isotope and element types:
relax> spin.isotope(isotope='15N', spin_id='@N', force=True)
relax> spin.isotope(isotope='1H', spin_id='@H', force=True)
relax> spin.element(element='N', spin_id=':*@N', force=True)
4. Define NH pairs:
relax> dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
Magnetic dipole-dipole interactions are now defined for the following spins:
# Spin_ID_1 Spin_ID_2
':6@N' ':6@H'
':7@N' ':7@H'
.
.
.
5. set the distance between N and H in the NH:
relax> dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02e-10)
Traceback (most recent call last):
File "gui/interpreter.pyc", line 299, in run
File "generic_fns/dipole_pair.pyc", line 237, in set_dist
File "generic_fns/interatomic.pyc", line 234, in interatomic_loop
KeyError: '#1shg-H_mol1:7@N'
What I didn't mention in my mail: I also imported all relaxation data files
(attached: out_files.zip). I can't tell which step of the process this was. If
I really just do the above, everything seems to work fine.
The relax state with the relaxation data included can be found attached, if
you want to have a look (the field strengths are not correct, only approximate
for the test). This state gives me reproducably the error message. You just
need to load it and click through the dipolar interaction dialog. So maybe you
can find soemthing in there.
The same state still loaded, with the relaxation data deleted one by one gives
the same error message as above. However, after saving the state, loading it
into relax again I needed to setup element and isotope again. Now it does NOT
give the error message.
I hope that helps.
(( P.S.: After loading the above file (state2.bz2), sometimes another error
comes up. Clicking the dipolar relaxation button, skipping through the
PDB-related parts, and clicking „Next“ in the panel where the pairs are
set up, I get several empty windows with just a „Cancel“ button (see
screen shot attached). After trying to setup the dipole pair, I still get the
error message. I am not sure how to reproduce that. ))
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Wed 25 Jul 2012 01:21:12 PM GMT Name: state2.bz2 Size: 25kB By: mab
<http://gna.org/bugs/download.php?file_id=16192>
-------------------------------------------------------
Date: Wed 25 Jul 2012 01:21:12 PM GMT Name: out_files.zip Size: 10kB By:
mab
<http://gna.org/bugs/download.php?file_id=16193>
-------------------------------------------------------
Date: Wed 25 Jul 2012 01:21:12 PM GMT Name: Screen Shot 2012-07-25 at
15.04.26.png Size: 23kB By: mab
<http://gna.org/bugs/download.php?file_id=16194>
_______________________________________________________
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<http://gna.org/bugs/?19982>
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