On 12 November 2015 at 19:00, Alain Oregioni <Alain.Oregioni@xxxxxxxxxxx>
wrote:
Hi,
I'm new to Relax and I'm having some trouble running a model free analysis
with my data. In short, all the spins are being deselected, supposedly
because of missing structural data even though I have loaded a PDB of the
structure.
Some details of the system:
I'm using Relax 4.0.0 with scripts under Win7 Pro 64
The molecule is a homodimer and I have R1, R2, hetNOE data at 600 and 700
MHz
The data is only from 5 spins out of 31 (for a chain, both chains being
identical)
The pdb is from a crystal structure (so, no proton)
What I've done so far:
I've run the dauvergne_protocol.py with 'local_tm' and 'sphere' without
problem. 'sphere' converged after 5 rounds. Both gave 'aic' solutions (but
then, I think they are not using the PDB directly).
However, when I run any of 'prolate', 'oblate', 'ellipsoid', the script end
up with "no model selected...'aic' pipe not created".
Looking at the console output, it seems that after the data is loaded fine
and dAuvergne_protocol() starts:
- pipe is created OK
- local_tm is read OK
- model_free.remove_tm() is run OK
- diffusion_tensor.init() is run OK
- fix() is run OK
Then:
- minimise.grid_search() starts and deselects all the spins: "Over-fit spin
deselection... because of missing structural data"
Of course, after this, the grid search does not work.
I'm thinking that my system is far from standard for this type of analysis,
and there are a few possibilities for things going wrong, starting with the
fact it's a homodimer, and that the spins with data are in limited numbers
(although they are spatially well distributed). But I have no ideas
how/where/why, so I'm a bit stuck for now. Does anyone have an idea?
I've attached a screenshot and the first 3 scripts in case that helps. If
you need anything else, please ask.
Hi Alain,
Welcome to the relax mailing lists! Have you managed to work out what
the problem was? I would suggest looking at your log file (you should
really run relax with the --log or --tee options to capture
everything). Look at the very top of the log for any warnings. This
type of error is almost always visible as a warning in the set up
stage of the analysis. Specifically where the structural data is
loaded into the relax data store. There is probably a mismatch
between the X and H spins and how they are named in the PDB file.
What are the first few lines of your analysis script?
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I've also noticed something that's probably not related, but just in case:
it seems that the function minimise.grid_search() starts with 'inc=11' even
if I passed 'GRID_INC=13' in my script (through dAuvergne_protocol() )...If
it's not expected, and other variables are somehow not updated, this might
be the cause of the problems.
If you have a look at the auto_analyses/dauvergne_protocol.py file (
http://www.nmr-relax.com/api/4.0/auto_analyses.dauvergne_protocol-module.html
), you see another option called 'diff_tensor_grid_inc' which defaults
to {'sphere': 11, 'prolate': 11, 'oblate': 11, 'ellipsoid': 6}. This
is where this number of 11 comes from. See the file itself for more
details.
Regards,
Edward
Re: model free analysis: spin deselection problem