Welcome to the GitHub page of the ViSCa code: a toolbox for performing Vibrational Spectroscopy Calculations. Like the golden bough (golden like a mistletoe; "viscum") that showed Aeneis where to find the entrance to the underworld where he would obtain words of wisdom from his father residing in the Elysian fields (see https://en.wikipedia.org/wiki/The_Golden_Bough_(mythology), and at the bottom of this readme file), we hope that the ViSCa tools on this page may help scientists interpret their vibrational spectroscopy datasets.
Currently users can download the following tools:
Vibrational sum-frequency generation (VSFG) spectroscopy:
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Code to calculate the orientation-dependency of the VSFG response to the protein orientation of a given protein structure (in PDB format). Spectral match in the amide-I region w.r.t. experimental data can be visualized in a so-called 2D-RSS plot (see ), and at the best-matching grid point in orientaion space, fits can be performed to finetune the spectral parameters and thus the match.
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The frame-selection method (see ) that allowsshe electhe selection of frames from a molecular dynamics (MD) simulation, based on the spectral match in the amide-I region.
2DIR:
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2DIR spectra calculation based on PDB input files
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2DIR spectra calculation and frame-selection method for MD frames (work in progress)
Vibrational circular dichroism (VCD):
- Clean-up of the code is in progress; will upload final code soon.
Sum-freqency scattering (SFS):
- Code to calculate sum-freqency scattering spectra in the amide-I region; will upload soon.
Further details about the code's name
As Virgil wrote between 29 and 19 BC, in his epic Aeneid (book VI): tollunt se celeres liquidumque per aera lapsae sedibus optatis gemina super arbore sidunt, discolor unde auri per ramos aura refulsit. quale solet siluis brumali frigore uiscum
Translation into English by Robert Fitzgerald (see https://llewelynmorgan.com/2013/10/03/au/):
What signs the doves might give, or where their flight Might lead him. And they fed, and then flew on, Each time as far as one who came behind Could keep in view. Then when they reached the gorge Of sulphurous Avernus, first borne upward Through the lucent air, they glided down To their desired rest, the two-hued tree Where glitter of gold filtered between green boughs. Like Mistletoe…
Interested readers are recommended to visit Llewely Morgan's website to read why the "discolor unde auri per ramos aura refulsit" line has received so much attention in classical language studies.