Hi Sam,
Welcome to the relax mailing lists. Sorry for the late reply, I've
been quite busy for the last two months. Please see below:
On 2 July 2016 at 02:41, Mahdi, Sam <sam.mahdi....@my.csun.edu> wrote:
> 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 guess you mean reading the spin system from a PDB file. You can do
this when running the structure.load_spins user function via the
spin_id parameter:
http://www.nmr-relax.com/manual/structure_load_spins.html
Or you can do this afterwards, either using the deselect.spin or
spin.delete user functions:
http://www.nmr-relax.com/manual/deselect_spin.html
http://www.nmr-relax.com/manual/spin_delete.html
> 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?
If this is a model-free analysis, the residues without data will be
automatically deselected prior to optimisation (you'll see this in the
logs).
> 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.
Ah, I think you might be confusing the loading of a structural file
and the creation of NMR-active spin systems. All atoms of the
structural file will be loaded into relax, but none of these atoms
will be set a spin systems. You then have to use the
structure.load_spins user function to pick our the NH atoms pairs of
interest.
> 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.
This is not correct. The proton relaxation values will be very
different. Note that almost no one collects this data as the proton
spin cannot be considered as isolated. Therefore the normal
assumptions for a model-free analysis of an isolated two spin system
do no hold. E.g. spin diffusion is an important effect in protons.
This is also why carbon relaxation and model-free analyses are only
performed at natural abundance, to ensure that the system is isolated.
> 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
You should simply not load any data for the proton. Then the analysis
will deselect those H spins prior to optimisation, if they haven't
already been deselected.
> 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.
That will be the warning, not error, that you should see. All protons
should be deselected.
> 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.
You should simply not set the proton relaxation data, and allow relax
to produce RelaxWarnings when the protons are deselected. You simply
need the proton information to set up the correct relaxation mechanism
for the nitrogen, and to indicate that this is an isolated two spin
system. I hope this helps.
Regards,
Edward
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