pucker
Calculate ring pucker using five or six points.
pucker [<name>] <mask1> <mask2> <mask3> <mask4> <mask5> [<mask6>] [geom] [out <filename>] [altona | cremer] [amplitude] [theta] [range360] [offset <offset>]
<name> Output data set name.
<maskX> Five (optionally six) atom masks selecting atom(s) to calculate pucker for.
[geom] Use geometric center of atoms in <maskX> (default is center of mass).
[out <filename>] Output file name.
[altona] Use method of Altona & Sundaralingam (5 masks only).
[cremer] Use method of Cremer and Pople (5 or 6 masks).
[amplitude] Also calculate amplitude.
[theta] (6 masks only) Also calculate theta.
[range360] Wrap pucker values from 0.0 to 360.0 (default is -180.0 to 180.0).
[offset <offset>] Add <offset> to pucker values.
Data Sets Created:
<name> Pucker in degrees.
<name>[Amp] Amplitude (if amplitude was specified).
<name>[Theta] Theta (if theta and 6 masks were specified).
Calculate the pucker (in degrees) for atoms in <mask1>, <mask2>, <mask3>, <mask4>, <mask5> using the method of Altona & Sundarlingam[ref1 and ref2] (default, or if altona specified), or the method of Cremer & Pople if cremer is specified. If <mask6> is specified calculate the pucker (and optionally theta if theta specified) according to the method of Cremer & Pople. If the amplitude keyword is given, amplitudes will be calculated in addition to pucker. The results from pucker can be further analyzed with the statistics analysis. By default, pucker values are wrapped to range from -180 to 180 degrees. If the range360 keyword is specified values will be wrapped to range from 0 to 360 degrees. Note that the Cremer & Pople convention is offset from Altona & Sundarlingam convention (with nucleic acids) by +90.0 degrees; the offset keyword will add an offset to the final value and so can be used to convert between the two. For example, to convert from Cremer to Altona specify “offset 90”.
To calculate nucleic acid pucker specify C1’ first, followed by C2’, C3’, C4’ and O4’.
For example, to calculate the sugar pucker for nucleic acid residues 1 and 2 using the method of Altona & Sundarlingam, with final pseudorotation values ranging from 0 to 360:
pucker p1 :1@C1’ :1@C2’ :1@C3’ :1@C4’ :1@O4’ range360 out pucker.dat pucker p2 :2@C1’ :2@C2’ :2@C3’ :2@C4’ :2@O4’ range360 out pucker.dat