Difference between revisions of "Pcs combi fit.m"
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{{DISPLAYTITLE:pcs_combi_fit.m}} __NOTOC__ | {{DISPLAYTITLE:pcs_combi_fit.m}} __NOTOC__ | ||
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Combinatorial PCS fitting function. This function takes into account potential ambiguities in diamagnetic and paramagnetic NMR assignments. | Combinatorial PCS fitting function. This function takes into account potential ambiguities in diamagnetic and paramagnetic NMR assignments. | ||
==Syntax== | ==Syntax== | ||
| − | |||
| − | = | + | [d_shifts,p_shifts,pcs_theo,pcs_expt,chi,total_theo]=pcs_combi_fit(parameters) |
| − | parameters.hfcs - cell array of 3x3 hyperfine tensors, | + | ==Parameters== |
| + | |||
| + | parameters.hfcs - cell array of 3x3 hyperfine tensors, | ||
in Gauss, usually out of gparse() or | in Gauss, usually out of gparse() or | ||
something similar | something similar | ||
| − | + | ||
| − | |||
| − | |||
parameters.isotopes - cell array of isotope specificati- | parameters.isotopes - cell array of isotope specificati- | ||
ons, e.g. {'1H','1H'} | ons, e.g. {'1H','1H'} | ||
| − | + | ||
parameters.spin_groups - cell array of integer vectors | parameters.spin_groups - cell array of integer vectors | ||
specifying the numbers of spins | specifying the numbers of spins | ||
| − | that have each of the chemical | + | that have each of the chemical |
| − | shifts specified, e.g. | + | shifts specified, e.g. |
{[28 22 30]; [25 33 81]} | {[28 22 30]; [25 33 81]} | ||
| − | + | ||
parameters.d_shifts - a vector of unique diamagnetic che- | parameters.d_shifts - a vector of unique diamagnetic che- | ||
mical shifts, in ppm | mical shifts, in ppm | ||
| − | + | ||
| − | parameters.p_shifts - a vector of unique paramagnetic | + | parameters.p_shifts - a vector of unique paramagnetic |
chemical shifts, in ppm | chemical shifts, in ppm | ||
| − | + | ||
parameters.d_ambig - a cell array of integer vectors spe- | parameters.d_ambig - a cell array of integer vectors spe- | ||
cifying the spins for which the dia- | cifying the spins for which the dia- | ||
magnetic assignment can potentially | magnetic assignment can potentially | ||
be swapped around. | be swapped around. | ||
| − | + | ||
parameters.p_ambig - a cell array of integer vectors spe- | parameters.p_ambig - a cell array of integer vectors spe- | ||
cifying the spins for which the para- | cifying the spins for which the para- | ||
| Line 42: | Line 40: | ||
==Outputs== | ==Outputs== | ||
| − | d_shifts - diamagnetic chemical shifts, optimally permuted | + | d_shifts - diamagnetic chemical shifts, optimally permuted |
p_shifts - paramagnetic chemical shifts, optimally permuted | p_shifts - paramagnetic chemical shifts, optimally permuted | ||
| Line 58: | Line 56: | ||
==Examples== | ==Examples== | ||
| − | |||
See combi_fit_1.m and combi_fit_2.m files in examples/nmr_paramag directory. | See combi_fit_1.m and combi_fit_2.m files in examples/nmr_paramag directory. | ||
==Notes== | ==Notes== | ||
| − | |||
Complexity scaling of the combinatorial procedure is very steep - specifying more than seven ambiguous atoms is not a good idea. | Complexity scaling of the combinatorial procedure is very steep - specifying more than seven ambiguous atoms is not a good idea. | ||
==See also== | ==See also== | ||
| − | + | [[ppcs.m]], [[lpcs.m]], [[kpcs.m]], [[ipcs.m]], [[centroid.m]], [[csa2racs.m]], [[eqmag.m]], [[fieldscan_enlev.m]], [[fieldscan_magn.m]], [[geffect.m]], [[hfc2pcs.m]], [[hfc2pms.m]], [[ippcs.m]], [[pcs2chi.m]], [[pms2chi.m]], [[probmax.m]], [[Built-in_experiments]] | |
| − | [[ppcs.m]], [[lpcs.m]], [[kpcs.m]], [[ipcs.m]] | ||
| − | |||
''Version 2.1, authors: [[Ilya Kuprov]], [[Elizaveta Suturina]]'' | ''Version 2.1, authors: [[Ilya Kuprov]], [[Elizaveta Suturina]]'' | ||
Latest revision as of 07:04, 30 August 2026
Combinatorial PCS fitting function. This function takes into account potential ambiguities in diamagnetic and paramagnetic NMR assignments.
Syntax
[d_shifts,p_shifts,pcs_theo,pcs_expt,chi,total_theo]=pcs_combi_fit(parameters)
Parameters
parameters.hfcs - cell array of 3x3 hyperfine tensors,
in Gauss, usually out of gparse() or
something similar
parameters.isotopes - cell array of isotope specificati-
ons, e.g. {'1H','1H'}
parameters.spin_groups - cell array of integer vectors
specifying the numbers of spins
that have each of the chemical
shifts specified, e.g.
{[28 22 30]; [25 33 81]}
parameters.d_shifts - a vector of unique diamagnetic che-
mical shifts, in ppm
parameters.p_shifts - a vector of unique paramagnetic
chemical shifts, in ppm
parameters.d_ambig - a cell array of integer vectors spe-
cifying the spins for which the dia-
magnetic assignment can potentially
be swapped around.
parameters.p_ambig - a cell array of integer vectors spe-
cifying the spins for which the para-
magnetic assignment can potentially
be swapped around.
Outputs
d_shifts - diamagnetic chemical shifts, optimally permuted
p_shifts - paramagnetic chemical shifts, optimally permuted
pcs_theo - theoretical pseudocontact shifts
pcs_expt - experimental pseudocontact shifts from optimally
permuted assignments
chi - rank 2 part of the magnetic susceptibility tensor,
in cubic Angstrom
total_theo - theoretical total NMR chemcial shifts, computed
as a sum of d_shifts and pcs_theo
Examples
See combi_fit_1.m and combi_fit_2.m files in examples/nmr_paramag directory.
Notes
Complexity scaling of the combinatorial procedure is very steep - specifying more than seven ambiguous atoms is not a good idea.
See also
ppcs.m, lpcs.m, kpcs.m, ipcs.m, centroid.m, csa2racs.m, eqmag.m, fieldscan_enlev.m, fieldscan_magn.m, geffect.m, hfc2pcs.m, hfc2pms.m, ippcs.m, pcs2chi.m, pms2chi.m, probmax.m, Built-in_experiments
Version 2.1, authors: Ilya Kuprov, Elizaveta Suturina
