Hi Edward,
thank you for your quick response. Thanks also for your help.
There's still a problem when trying to setup the dipole pair, maybe I
messed something up:
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'
I don't really know what that means.
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'
So I don't know where this comes from. The NH pairs are set up, and
dipole_pair.set_dist takes just the three parameters. Oddly, relax does not
complain about the first residue (6), but the second in the sequence (7).
From how it shows up in the spin editor, there is actually no difference
between the two.
The relax state can be found here, if you want to have a look:
https://www.dropbox.com/s/heukkeycpwzsvmb/state2.bz2
I'd appreciate your support :)
Regards
Martin
On 24.07.2012, at 16:20, Edward d'Auvergne wrote:
Hi Martin,
In the new relax versions, you'll have to do things a little
differently. In the case where no structure is available, you can
just click on the 'Skip' buttons for the structural parts of the
dipolar relaxation wizard. I was thinking about having a page at the
start of the wizard to ask if structural data is available, and use
this to skip the 2 structure related wizard pages (structure.read_pdb
and structure.get_pos), but it's a lot of effort considering most
users will have a 3D structure. Note that you'll also have to have
both proton and nitrogen spins set up in the new relax versions to
define the magnetic dipole-dipole interaction. This will allow
multi-pole relaxation support to be added to relax in the future.
I hope this info helps. You may encounter other problems in the GUI
if you don't have a structure. The flexibility of the scripting mode
is lost in the GUI, so it is hard to bring back all the features into
the GUI. But relax will handle an analysis without a structure.
Regards,
Edward
On 24 July 2012 16:05, Martin Ballaschk <ballaschk@xxxxxxxxxxxxx> wrote:
Hi Edward,
I was wondering if it is possible to run relaxGUI's model-free routine if
there is no structure model available. Of course, only the local_tm or
spherical "global" models could be used for an analysis, then.
In the current 2.1.0 release, the user is forced to load a structure file
("dipolar relaxation" button). Shouldn't relax run without loading any
structural information if I select "sphere" or "local_tm" in the protocol
mode field? Looking at the sample scripts in the manual, this could
easily be done via a relax script (I haven't tried), but is it possible
also via the GUI?
Cheers
Martin
Re: relaxGUI, local_tm / sphere and the need for a structure model