Hi,
Thanks for you reply.
My chemical shift table syntax seems to be fine.
I added the line
xplor.command('prot print threshold 0.0 all norm end')
after setting up the term and still could not get the calculation to run.
Here is the part of the output:
X-PLOR>prot print threshold 0.0 all norm end
The following proton delta shifts are
greater than the cutoff:
(proton)(delta)(calc)(obs)(rcoil)(magn anis)(elec)
class ALPH
A 20 ASP HA 0.445 5.135 4.690 4.120 1.022 -0.008 0.000
A 21 LYS HA 0.081 4.301 4.220 3.710 0.583 0.009 0.000
A 22 GLU HA 0.024 4.294 4.270 3.650 0.628 0.016 0.000
A 23 GLU HA 0.038 4.348 4.310 3.650 0.682 0.016 0.000
A 24 CYS HA 0.187 5.007 4.820 4.040 0.972 0.049 -0.054
A 25 THR HA 0.142 4.442 4.300 3.700 0.811 0.036 -0.105
A 26 VAL HA 0.197 4.147 3.950 3.530 0.941 0.011 -0.335
A 27 PRO HA 0.339 4.349 4.010 3.820 0.520 -0.008 0.017
A 28 ILE HA 0.259 4.489 4.230 3.570 0.599 0.031 0.289
A 30 TRP HA 2.030 5.610 3.580 4.450 0.869 0.016 0.274
A 31 SER HA 0.139 4.129 3.990 3.850 0.440 -0.048 -0.113
A 32 GLU HA 0.239 4.299 4.060 3.650 0.791 0.035 -0.178
A 33 PRO HA 0.204 3.924 3.720 3.820 0.494 -0.021 -0.369
A 34 VAL HA 0.087 4.397 4.310 3.530 0.897 0.033 -0.062
A 35 LYS HA -0.006 4.184 4.190 3.710 0.965 0.034 -0.525
A 37 LEU HA -0.656 3.994 4.650 3.740 0.413 -0.082 -0.077
A 38 CYS HA 0.652 4.932 4.280 4.040 0.897 0.057 -0.063
A 39 LYS HA -0.041 4.379 4.420 3.710 0.707 0.032 -0.070
A 40 ALA HA -1.307 3.543 4.850 3.700 0.253 -0.086 -0.324
A 41 ARG HA -0.683 3.787 4.470 3.750 0.082 -0.014 -0.030
A 42 PHE HA 0.398 5.088 4.690 4.450 0.333 -0.124 0.429
A 43 THR HA 0.213 4.513 4.300 3.700 0.818 -0.040 0.035
A 44 ARG HA -0.165 4.785 4.950 3.750 0.920 0.226 -0.111
A 45 TYR HA 0.760 5.520 4.760 4.450 0.911 0.087 0.072
A 46 TYR HA 0.817 5.627 4.810 4.450 0.962 -0.019 0.234
A 47 CYS HA 1.269 5.039 3.770 4.040 0.793 0.086 0.121
RMS error = NaN
Number of violations: 26.000
The calculated and observed proton chemical shifts are quite different.
I have changed the threshold in
xplor.command('prot print threshold 2.05 all norm end') to test whether it
would work when the number of violations are zero.
I have also tried
xplor.command('prot print threshold 2.05 class alpha NORMsd end')
and
xplor.command('prot print threshold 2.05 class alpha RMSD end')
but neither have worked.
If you could also explain what the columns proton and delta are it would be of
great help.
Thanks,
Ishita
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