---------- Forwarded message ---------- From: Mahdi, Sam <sam.mahdi....@my.csun.edu> Date: Fri, Jul 1, 2016 at 4:56 PM Subject: Troubleshooting model-free analysis To: relax-users@gna.org
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. _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users