I had 2 questions regarding the relax model-free analysis.
1: When uploading a pdb file for the spin system, is there a certain way to
have some residues spins ignored? i.e. give it a certain range. E.g. The
structural data for the pdb file I want uses an extra linker at the
C-terminus of my protein that is about 7 residues long. The relaxation data
I have however is for the protein without those 7 extra residues (thus
residue 7 for the pdb file is residue 1 for my relaxation data). Is there a
way I can get the relax program to ignore the first 7 residues? I tried
typing in the range I wanted (residue 8 to residue 133 inputed as [8-133])
in the molecule number to read option, but when I did that, it gave me this
error RelaxError: No PDB file has been loaded. When I removed the range, it
uploaded the file but with all the residues, including the linker I didn't
want.
2: The relaxation data I have is for the backbone (NH), thus the values I
have for the backbone are for that bond. The pdb file I uploaded has both
of their spins. The relaxation data I have is one value for each residue
(for the NH bond). So I assumed that value is the same for both the
Nitrogen and Hydrogen spin of that residue. E.g. If residue 3 has a R1
value of 1.03, I assume the nitrogen spin and hydrogen spin both have an R1
value of 1.03. When I upload the relaxation data with the Nitrogen @N spin
id string it works fine, each residue has the proper value. However, the
value for the hydrogen is 0 for each residue. I tried to create a new data
set, this time with the spin id string for Hydrogen using the same R1 file
I had used for the nitrogen, but when I did this I was given this error:
RelaxWarning: The sequence data in the line ['Residue', 'R1', 'Error'] is
invalid, the residue number data 'Residue' is invalid.
RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
error data is missing.
RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
error data is missing.
RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
error data is missing.
RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
error data is missing.
RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
error data is missing.
Traceback (most recent call last):
File "/usr/local/Relax/relax-2.2.5/gui/wizard.py", line 163, in _apply
self.exec_status = self.on_execute()
File "/usr/local/Relax/relax-2.2.5/gui/uf_objects.py", line 867, in
on_execute
return_status = self.execute(self.name, **kargs)
File "/usr/local/Relax/relax-2.2.5/gui/uf_objects.py", line 797, in
execute
return_status = interpreter.apply(uf, *args, **kwds)
File "/usr/local/Relax/relax-2.2.5/gui/interpreter.py", line 112, in apply
apply(fn, args, kwds)
File "/usr/local/Relax/relax-2.2.5/generic_fns/relax_data.py", line 1033,
in read
pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names,
res_nums=res_nums, res_names=res_names, spin_nums=spin_nums,
spin_names=spin_names, spin_id=spin_id)
File "/usr/local/Relax/relax-2.2.5/generic_fns/relax_data.py", line 870,
in pack_data
new_id = new_ids[0]
IndexError: list index out of range
I don't know why it states the sequence data in the ling [0,0] is invalid
with missing error data. It is the same file I used for the nitrogen and
that worked fine. If I do not upload a hydrogen file, naturally when relax
is run, I will recieve an error stating that every single hydrogen spin has
been deselected due to the absence of data, and then it'll stop the
simulations.
Extra info:
this is how the script looks when I upload it with the NItrogen Id string
elax> relax_data.display(ri_id='R1_NMRFAM')
# mol_name res_num res_name spin_num spin_name
value error
hRGS7 1 GLY 1
N 0 0
hRGS7 2 SER 8
N 0 0
hRGS7 2 SER 14 H
None None
hRGS7 3 SER 19
N 0 0
hRGS7 3 SER 25 H
None None
hRGS7 4 GLY 30
N 0 0
hRGS7 4 GLY 34 H
None None
hRGS7 5 SER 37
N 1.15 0.03
hRGS7 5 SER 43 H
None None
hRGS7 6 SER 48
N 0.832 0.011
hRGS7 6 SER 54 H
None None
hRGS7 7 GLY 59
N 1.07 0.05
hRGS7 7 GLY 63 H
None None
hRGS7 8 SER 66
N 0.78 0.17
hRGS7 8 SER 72 H
None None
hRGS7 9 GLN 77
N 0 0
hRGS7 9 GLN 86 H
None None
hRGS7 10 GLN 94
N 0 0
hRGS7 10 GLN 103 H
None None
hRGS7 11 ARG 111
N 0 0
hRGS7 11 ARG 122 H
None None
hRGS7 12 VAL 135
N 1.26 0.03
hRGS7 12 VAL 142 H
None None
hRGS7 13 LYS 151
N 0.899 0.023
hRGS7 13 LYS 160 H
None None
hRGS7 14 ARG 173
N 0.854 0.009
hRGS7 14 ARG 184 H
None None
hRGS7 15 TRP 197
N 0.99 0.04
hRGS7 15 TRP 211 H
None None
hRGS7 16 GLY 221
N 0 0
hRGS7 16 GLY 225 H
None None
hRGS7 17 PHE 228
N 0.894 0.016
hRGS7 17 PHE 239 H
None None
hRGS7 18 GLY 248
N 0.874 0.014
hRGS7 18 GLY 252 H
None None
hRGS7 19 MET 255
N 0 0
hRGS7 19 MET 263 H
None None
hRGS7 20 ASP 272
N 0 0
hRGS7 20 ASP 280 H
None None
hRGS7 21 GLU 284
N 0 0
hRGS7 21 GLU 293 H
None None
hRGS7 22 ALA 299
N 0.939 0.022
As you can see, the hydrogen values it states none, while giving the
relaxation value to the nitrogen.
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