MRSimulator MCP

Tools 13

• mrsimulator__toggle_multi_site_spectype
• mrsimulator__toggle_single_site_quad_fields Show AND zero the quadrupolar fields together when switching back to spin-1/2 - not just hide them. A hidden Gradio field still submits its last value on the next click; if Cq were left at a leftover nonzero value while merely hidden, simulate_powder_pattern would try to attach quadrupolar coupling to a spin-1/2 nucleus and mrsimulator correctly rejects that outright. Reproduced directly: clicking Simulate on this tab's own un-touched defaults raised exactly that ValidationError, which is what this fixes.
• mrsimulator_simulate_amorphous_distribution Simulate the powder pattern of a disordered/amorphous site, whose tensor parameters (quadrupolar or shielding) follow a Czjzek or extended-Czjzek random distribution rather than a single fixed value. The isotropic chemical shift is ALSO distributed (an independent Gaussian, matching the source paper's Eq. 60-61, joined with the anisotropy distribution to form the full 3D distribution of Fig. 3) - checked directly that this needed adding: mrsimulator's CzjzekDistribution/ExtCzjzekDistribution classes only draw the anisotropy (zeta or Cq) and eta; their mean_isotropic_chemical_shift constructor argument is not actually applied by .rvs() at all, so without this, every sampled site would share one exact isotropic value and the amorphous lineshape would be missing a real, often significant broadening contribution. IMPORTANT for the calling agent: this tool's result includes a text line reading "Image URL: <url>" alongside the image data. Take that url and relay it in your reply as markdown
• mrsimulator_simulate_coupled_multi_site_spectrum Simulate a system of 3 or more weakly J/dipolar-coupled sites (e.g. a homonuclear or heteronuclear AMX system), generalizing simulate_coupled_two_site_spectrum beyond a single pair. Any number of sites and any subset of pairwise couplings between them is allowed. IMPORTANT for the calling agent: this tool's result includes a text line reading "Image URL: <url>" alongside the image data. Take that url and relay it in your reply as markdown image syntax,  - do not just mention the url as plain text or describe the image instead. Some clients only display images embedded this way in the visible reply; images left inside the raw tool result are not shown to the user on those clients.
• mrsimulator_simulate_coupled_two_site_spectrum Simulate the spectrum of two coupled sites (J-coupling and/or direct dipolar coupling), e.g. a 1H-13C pair with a one-bond J coupling, or two dipolar-coupled 1H sites. IMPORTANT for the calling agent: this tool's result includes a text line reading "Image URL: <url>" alongside the image data. Take that url and relay it in your reply as markdown image syntax,  - do not just mention the url as plain text or describe the image instead. Some clients only display images embedded this way in the visible reply; images left inside the raw tool result are not shown to the user on those clients.
• mrsimulator_simulate_mqmas_multi_site_spectrum Simulate a 2D multi-quantum MAS (MQ-VAS) correlation spectrum for SEVERAL quadrupolar sites at once - generalizes simulate_mqmas_spectrum beyond a single site. This matters because resolving overlapping quadrupolar sites via 2D correlation is usually the actual point of running MQMAS in the first place (e.g. the three crystallographically distinct sites of RbNO3, or several aluminosilicate sites) - a single-site-only tool missed that. IMPORTANT for the calling agent: this tool's result includes a text line reading "Image URL: <url>" alongside the image data. Take that url and relay it in your reply as markdown image syntax,  - do not just mention the url as plain text or describe the image instead. Some clients only display images embedded this way in the visible reply; images left inside the raw tool result are not shown to the user on those clients.
• mrsimulator_simulate_mqmas_spectrum Simulate a 2D multi-quantum MAS (MQ-VAS) correlation spectrum for a quadrupolar nucleus, separating isotropic and second-order quadrupolar anisotropic broadening onto two axes. IMPORTANT for the calling agent: this tool's result includes a text line reading "Image URL: <url>" alongside the image data. Take that url and relay it in your reply as markdown image syntax,  - do not just mention the url as plain text or describe the image instead. Some clients only display images embedded this way in the visible reply; images left inside the raw tool result are not shown to the user on those clients.
• mrsimulator_simulate_multi_site_spectrum Simulate a multi-site NMR spectrum (e.g. several crystallographic sites of a published compound), with relative abundances. Each site may include chemical-shift anisotropy, quadrupolar coupling, or both, plus the relative orientation between the two tensors if a site has both (see simulate_powder_pattern for how much that can matter). IMPORTANT for the calling agent: this tool's result includes a text line reading "Image URL: <url>" alongside the image data. Take that url and relay it in your reply as markdown image syntax,  - do not just mention the url as plain text or describe the image instead. Some clients only display images embedded this way in the visible reply; images left inside the raw tool result are not shown to the user on those clients.
• mrsimulator_simulate_powder_pattern Simulate a single NMR site (powder pattern), static or under MAS (or off-magic-angle VAS). Supports chemical-shift anisotropy and/or quadrupolar coupling, including the relative orientation between the two tensors when a site has both (real crystal sites rarely have coincident shielding and electric-field-gradient tensors). Verified directly that this orientation genuinely changes the simulated spectrum (not a no-op): for a 2H site with both interactions, beta=0 vs beta=90 degrees gives visibly different lineshapes. IMPORTANT for the calling agent: this tool's result includes a text line reading "Image URL: <url>" alongside the image data. Take that url and relay it in your reply as markdown image syntax,  - do not just mention the url as plain text or describe the image instead. Some clients only display images embedded this way in the visible reply; images left inside the raw tool result are not shown to the user on those clients.
• mrsimulator_simulate_sideband_correlation_2d Simulate a 2D isotropic/anisotropic sideband-correlation spectrum (a PASS/MAT-type experiment), separating the isotropic position from the spinning-sideband pattern onto two axes. Optionally also gives the site quadrupolar coupling, in which case the sidebands reflect BOTH the shielding anisotropy and the quadrupolar anisotropy of the same site at once - the relative orientation between the two tensors then matters and is exposed too (verified directly: changing it measurably changes the 2D pattern for a real test case). Known limitation, checked directly rather than assumed: this only works for half-integer quadrupolar spins (23Na, 27Al, ...). For integer spins (2H, I=1) the underlying SSB2D method fails outright ("need more than 1 value to unpack") - which matches the source paper's own note that I=1 needs special handling not provided by this general-purpose class (their Fig. 6 2H example uses a separate, hand-built treatment described in their supplementary material, not exposed as
• mrsimulator_simulate_sideband_correlation_2d_multi_site Simulate a 2D sideband-correlation spectrum for SEVERAL sites at once - generalizes simulate_sideband_correlation_2d beyond a single site, for the same reason as the MQ-MAS/ST-MAS multi-site tools: separating overlapping sideband manifolds from different sites is usually the actual point of running a 2D correlation instead of 1D. IMPORTANT for the calling agent: this tool's result includes a text line reading "Image URL: <url>" alongside the image data. Take that url and relay it in your reply as markdown image syntax,  - do not just mention the url as plain text or describe the image instead. Some clients only display images embedded this way in the visible reply; images left inside the raw tool result are not shown to the user on those clients.
• mrsimulator_simulate_stmas_multi_site_spectrum Simulate a 2D satellite-transition MAS (ST-VAS) correlation spectrum for SEVERAL quadrupolar sites at once - generalizes simulate_stmas_spectrum beyond a single site, for the same reason as simulate_mqmas_multi_site_spectrum: resolving several overlapping sites is usually the actual point. IMPORTANT for the calling agent: this tool's result includes a text line reading "Image URL: <url>" alongside the image data. Take that url and relay it in your reply as markdown image syntax,  - do not just mention the url as plain text or describe the image instead. Some clients only display images embedded this way in the visible reply; images left inside the raw tool result are not shown to the user on those clients.

All 13 tools