pseudorotation

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• Previous message: herbert_bernstein: "ensembles of entities"

This is in response to Dale's message about pseudorotation. While
he is correct that the Cremer and Pople form is more general and
would apply to all flexible rings, the Altona and Sundaralingam formalism
is widely used by the nucleic acid community. I suggest that it be included
in the struct_mon_nucl section. I am not exactly sure where the Cremer
and Pople one should go but I do agree that it too deserves a place.
I have written up the S and A ones for now.
-----------------------------------------------------------------------
save__struct_mon_nucl.tau2
    _item_description.description
;              The value in degrees of the sugar torsion angle tau2
               C1'_C2'_C3'_C4'.
;
    _item.name                  '_struct_mon_nucl.tau2'
    _item.category_id             struct_mon_nucl
    _item.mandatory_code          no
    _item_type.code               float
    _item_units.code             'degrees'
     save_

save__struct_mon_nucl.tau3
    _item_description.description
;              The value in degrees of the sugar torsion angle tau2
               C2'_C3'_C4'_O4'.
;
    _item.name                  '_struct_mon_nucl.tau3'
    _item.category_id             struct_mon_nucl
    _item.mandatory_code          no
    _item_type.code               float
    _item_units.code             'degrees'
     save_

save__struct_mon_nucl.tau4
    _item_description.description
;              The value in degrees of the sugar torsion angle tau4
               C3'_C4'_O4'_C1'.
;
    _item.name                  '_struct_mon_nucl.tau4'
    _item.category_id             struct_mon_nucl
    _item.mandatory_code          no
    _item_type.code               float
    _item_units.code             'degrees'
     save_

save__struct_mon_nucl.tau0
    _item_description.description
;              The value in degrees of the sugar torsion angle tau0
               C4'_O4'_C1'_C2'.
;
    _item.name                  '_struct_mon_nucl.tau0'
    _item.category_id             struct_mon_nucl
    _item.mandatory_code          no
    _item_type.code               float
    _item_units.code             'degrees'
     save_

save__struct_mon_nucl.tau1
    _item_description.description
;              The value in degrees of the sugar torsion angle tau1
               O4'_C1'_C2'_C3'.
;
    _item.name                  '_struct_mon_nucl.tau1'
    _item.category_id             struct_mon_nucl
    _item.mandatory_code          no
    _item_type.code               float
    _item_units.code             'degrees'
     save_

save__struct_mon_nucl.taum
    _item_description.description
;              The maximum amplitide of puckering. It is derived from the
               the pseudorotation value, P, and the torsion angles in the ribose
               ring.

               Tau2= Taum cosP
               Tau3= Taum cos(P+144)
               Tau4= Taum cos(P+288)
               Tau0= Taum cos(P+ 72)
               Tau1= Taum cos(P+216)
;
    _item.name                  '_struct_mon_nucl.taum'
    _item.category_id             struct_mon_nucl
    _item.mandatory_code          no
    _item_type.code               float
    _item_units.code             'degrees'
     save_

save__struct_mon_nucl.P
    _item_description.description
;              P is the phase angle of pseudorotation for five membered rings. 
               This formulation is used for ribo and deoxyribo sugars in nucleic
               acids.
                          (tau4 +tau1)-(tau3+tau0)
               P = ATAN (-------------------------)
                           2tau2 (sin 36+sin 72)

               If tau2 is <0, then P=P+180

               This formulation is by Altona and Sundaralingam (1972), J.A.C.S.,
               94, 8205-8212.
;
    _item.name                  '_struct_mon_nucl.taum'
    _item.category_id             struct_mon_nucl
    _item.mandatory_code          no
    _item_type.code               float
    _item_units.code             'degrees'
     save_


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