Few tips that will save your time when using Relax* (https://www.nmr-relax.com).
*d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119.
*d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133.
FILES to load: NOE, R1, R2, pdb
Format of NOE/Rs:
name of protein / number / residue / number / atom (N) / value / error
COMT 1 GLN 1 N 1.055199602 0.047908918
COMT 2 GLY 2 N 0.628859626 0.020470979
COMT 4 THR 4 N 0.649051411 0.023684093
COMT 5 LYS 5 N 0.668918693 0.04637887
Relax doesn't like negative values. Delete if you have any negative NOEs.
Format of pdb: must be with hydrogens!
ATOM 9 OE1 GLN A 1 13.151 31.068 48.151 1.00 51.60 O
ANISOU 9 OE1 GLN A 1 7933 4830 6844 575 2062 -440 O
ATOM 10 HA GLN A 1 17.757 30.808 49.407 1.00 0.00 H
ATOM 11 HB2 GLN A 1 15.798 29.870 50.273 1.00 0.00 H
ATOM 12 HB3 GLN A 1 15.231 31.229 49.293 1.00 0.00 H
Check your hydrogens. Must be named as HA, HB etc. In one file I had H01, H02 - didn't work then. And again Relax doesn't like negative values. If your numbering starts with negative value, change it!
Ex. in Pymol by : alter sele, resi=str(int(resi)-50) - it will subtract 50 from your numbering. "+" (adding) also works.
Special case - dimer pdb
If your pdb file is a dimer, then start numbering for the second chain by continuing numbering of first chain, ex:
ATOM 3632 HD2 PRO A 215 -10.765 0.092 78.087 1.00 0.00 H
ATOM 3633 HD3 PRO A 215 -11.387 -0.161 79.748 1.00 0.00 H
ATOM 3634 N GLN B 216 -32.761 14.719 114.374 1.00 17.47 N
ANISOU 3634 N GLN B 216 2676 1985 1976 -348
Pro was the last residue of chain A (number 215), Gln first of chain B (number 216 instead of 1).
*d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119.
*d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133.
FILES to load: NOE, R1, R2, pdb
Format of NOE/Rs:
name of protein / number / residue / number / atom (N) / value / error
COMT 1 GLN 1 N 1.055199602 0.047908918
COMT 2 GLY 2 N 0.628859626 0.020470979
COMT 4 THR 4 N 0.649051411 0.023684093
COMT 5 LYS 5 N 0.668918693 0.04637887
Relax doesn't like negative values. Delete if you have any negative NOEs.
Format of pdb: must be with hydrogens!
ATOM 9 OE1 GLN A 1 13.151 31.068 48.151 1.00 51.60 O
ANISOU 9 OE1 GLN A 1 7933 4830 6844 575 2062 -440 O
ATOM 10 HA GLN A 1 17.757 30.808 49.407 1.00 0.00 H
ATOM 11 HB2 GLN A 1 15.798 29.870 50.273 1.00 0.00 H
ATOM 12 HB3 GLN A 1 15.231 31.229 49.293 1.00 0.00 H
Check your hydrogens. Must be named as HA, HB etc. In one file I had H01, H02 - didn't work then. And again Relax doesn't like negative values. If your numbering starts with negative value, change it!
Ex. in Pymol by : alter sele, resi=str(int(resi)-50) - it will subtract 50 from your numbering. "+" (adding) also works.
Special case - dimer pdb
If your pdb file is a dimer, then start numbering for the second chain by continuing numbering of first chain, ex:
ATOM 3632 HD2 PRO A 215 -10.765 0.092 78.087 1.00 0.00 H
ATOM 3633 HD3 PRO A 215 -11.387 -0.161 79.748 1.00 0.00 H
ATOM 3634 N GLN B 216 -32.761 14.719 114.374 1.00 17.47 N
ANISOU 3634 N GLN B 216 2676 1985 1976 -348
Pro was the last residue of chain A (number 215), Gln first of chain B (number 216 instead of 1).
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