Hi Vitaly,
The problem here is not to do with the spin numbering. That is not
needed. I've now updated relax to print out the full spin ID string
instead of just the spin number and name. I've also modified the
error messages to be more informative. Could you update your
repository copy of relax and send the new error messages? Thanks.
One problem I see, though this may not be the cause of the error, is
in the reading of the relaxation data. The script line:
relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.484*1e6,
file='data.r1.600', mol_name_col=1, res_num_col=2, res_name_col=3,
spin_name_col=5)
should probably be:
relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.484*1e6,
file='data.r1.600', mol_name_col=1, res_num_col=2, res_name_col=3,
spin_name_col=5, data_col=6, error_col=7)
Specifying the data and error columns is very important. Though
according to the code, if the data and error were not read in, then
the checks resulting in the RelaxError should not occur. The problem
with the spin numbers is that the numbers in 'data.r1.600' do not
match the numbers in the first column of the PDB file. For proteins,
it is safe to not specify the spin number as all atoms of the residue
should have a different name. For small organic molecules, RNA, DNA,
sugars, etc, this is not the case. Anyway, the spin numbers in the
structural file and data files must match if they are used at all.
If you could, submitting a bug report would be appreciated
(https://gna.org/bugs/?func=additem&group=relax). This helps other
relax users if they encounter the same issue. If you could attach a
minimal script with a minimal data set (relaxation data for one or two
residues, randomised if you prefer), then I'll be able to quickly
reproduce the bug and normally fix it within 5 minutes. I would then
also be able to add the script and data to the relax test suite to
make sure that the bug never returns.
Cheers,
Edward
On 5 October 2011 01:48, V.V. <vvostri@xxxxxxxxx> wrote:
Hello,
It looks like Relax scripts changed a bit since the last time I used
it. I am trying to setup the initial test calculation with
"single_model.py", and running into problems with spins initialization
(revision 14778).
Sample input files:
=====
#mol_name res_num res_name spin_num spin_name data error
ave 1 Met 1 N None None
ave 2 Glu 2 N 1.8903 0.06062
...
=====
Script extract is below:
=====
name = 'tm1'
pipe.create(name, 'mf')
sequence.read('data.r1.600', mol_name_col=1, res_num_col=2,
res_name_col=3, spin_name_col=5)
structure.read_pdb('ave.pdb', read_mol=1, set_mol_name='ave',
parser='internal')
relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.484*1e6,
file='data.r1.600', mol_name_col=1, res_num_col=2, res_name_col=3,
spin_name_col=5)
#More data sets are loaded and other parameters initialized
Grid_search(inc=11)
=====
This returns an error:
"RelaxError: Negative error for spin 'None N', minimization not possible"
Is this because the "spin_number" has not been initialized during the
"sequence.read" and "relax_data.read"? If I try to use
"spin_num_col=4" in "sequence.read", then "structure.read" returns an
error: "RelaxWarning: Cannot find the atom in the structure (atom ID
':2@2&@N')"
Please let me know if you need more details.
Thank you,
Vitaly
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Re: RelaxError: Negative error for spin, minimization not possible