STRUCTURES

NAME
STRUCTURES - Compute the root mean square deviations from a given solute reference structure

SYNOPSIS

STRUCTURES
    ...
    ...
END

DESCRIPTION
The command STRUCTURES opens an environment which includes a series of subcommands which allow to compute average and instantaneous root mean square displacements (rms) of the solute for various atomic type ($\alpha$-carbon, heavy atoms, backbone atoms etc. ). The reference structure for the solute is entered with the command TEMPLATE(&SETUP)

averaged ca
compute average rms of $\alpha$-carbons

averaged heavy
compute average rms of non hydrogen atoms

inst_xmrms   type_1 type_2 ...
specifies which instantaneous rms's have to computed. type_n can be any combination of the four keywords ca heavy backbone allatoms. The keyword all stands for all the the preceding keywords simultaneously. The inst_xrms keyword is mandatory when print inst_xmrs is specified.

print type nprint   OPEN  filename
print rms's calculation as specified by type to file filename every nprint configurations (see also command DUMP(&INOUT)) The keyword type can be any of the following:

averaged - the full protein (solute) coordinates in pdb format are printed to the file filename with a constant orientation so that atomic rms's are minimized. Feeding directly the file to rasmol gives an pictorial view of the atomic displacements

avg_xrms - The time running averages of the rms's are printed, averaged over $\alpha$-carbons, backbone atoms, and all heavy atoms.

inst_xrms - The instantaneous values of the rms's are printed averaged over $\alpha$-carbons, backbone atoms, and all heavy atoms. If this subcommand is specified, along with inst_xmrms subcommand orac also produces the file filename_atm which contains the final values of the atomic rms's for the atom types ($\alpha$ carbon, backbone atoms etc. ) specified in the command inst_xrms.

EXAMPLES

STRUCTURES
  print averaged 2 OPEN test.str
  print avg_xrms  3 OPEN test.arms
  print inst_xrms  3 OPEN test.irms
  inst_xrms ca backbone
  averaged ca
  print rms 2 OPEN test.rms
END

WARNINGS
STRUCTURES commands works only in conjunction with the &ANALYSIS environment. Experimental - Unsupported