SCALar : commands to manipulate scalar atom properties
[SYNTAX SCALar]
SCALar keyname { } [atom-selection]
{ = keyname } ! do a copy of vectors
{ SET <real> } ! A = <real>
{ ADD <real> } ! A = <real> + A
{ MULT <real> } ! A = <real> * A
{ DIVI <real> } ! A = A / <real>
{ SIGN } ! A = sign ( A )
{ INTEger } ! A = int ( A )
{ RECIprocal } ! A = 1/ A
{ LOG } ! A = ln ( A )
{ EXP } ! A = exp ( A )
{ ABS } ! A = ABS ( A )
{ NORM } ! A = A / 2-norm(A)
{ MIN <real> } ! A = MIN (A,<real>)
{ MAX <real> } ! A = MAX(A,<real>)
{ POWEr <real> } ! A = A ** <real>
{ POW2r } ! A = A * A
{ IPOW <real> } ! A = A ** int(<real>), OK for neg A
{ SQRT } ! A = SQRT(A)
{ SHOW [SORT] }
{ STATistics weight_opt }
{ STORe store_number } ! S(i) = A(i)
{ RECAll store_number } ! A(i) = S(i)
{ +STOre store_number } ! S(i) = S(i) + A(i)
{ *STOre store_number } ! S(i) = S(i) * A(i)
{ READ <unit> }
{ }
{ [ ALL ] }
{ AVERage [ BYSEgment ] } ! S(i) = sum(S(j))/Nj
{ [ BYREsidue ] } ! averaged over each selected
{ [ BYGRoup ] } ! atom of each item
weight_opt
keyname ::= { X }
{ Y } ! (main coordinates)
{ Z }
{ WMAIn } ! (main coordinate weights)
{ XCOMp }
{ YCOMp } ! (comparison coordinates)
{ ZCOMp }
{ WCOMp } ! (comparison coordinate weights)
{ DX }
{ DY } ! (forces from last energy eval)
{ DZ }
{ ECONt } ! Energy partition array
{ EPCOnt } ! Free energy difference atom partition
{ MASS } ! (atom masses)
{ CHARge } ! (atom charges)
{ CONStraints } ! (harmonic constraint constants)
{ XREF }
{ YREF } ! (reference coordinates)
{ ZREF }
{ FBETa } ! (friction coefficients)
{ MOVE } ! (rigid constraints flag)
{ TYPE } ! (atom chemical type codes)
{ IGNOre } ! (ASP flag for ignoring atoms)
{ ASPValue } ! (ASP parameter value)
{ VDWSurface } ! (ASP van der Waals surface)
{ ALPHa (**) } ! (atom polarizability)
{ EFFEct (**) } ! (effective number of electrons)
{ RADIus (**) } ! (van der Waal radii)
store_number ::= any number between 1 and 9.
weight_opt ::= [ WEIGht store_number ] [MASS]
For the keynames labeled (**), the array values may not
be modified by any scalar command, but they may be used
in the SHOW and STORe operations.
All of the SCALar commands allow an atom selection.
The dimension of all vectors is equal to the number of atoms. (see the
vibrational analysis section for 3N vector manipulations).
The READ option reads from an ascii file all selected entries,
one value per line. This file should have a valid value within the first
40 characters of each line, and should not have a CHARMM title.
The STATistics and AVERage options accept a weighting option. If
not specified, all atoms will have an equal weighting. If specified, the
weighting of each atom will be in the specified stored vector. For the
AVERage option, the averaging may be done over ALL selected atoms, or over
groups of selected atoms defined be segment, residue, or group boundaries.
For example if one wants to print out the rms mass weighted
fluctutions for the sidechain of each residue, the sequence should
be something like;
COOR DYNA .... ! put the rms fluctuations in the weighting array
SCALar MASS STORe 1 ! put the masses in the first storage vector
SCALar WMAIn IPOW 2 ! convert rms fluctuation to mean squared fluctuations.
SCALar WMAIn AVERage BYREsidue WEIGht 1 SELE .NOT.
( TYPE CA .OR. TYPE C .OR. TYPE N .OR. TYPE H .OR. TYPE O ) END
! does the averaging for the sidechain with mass weighting
SCALar WMAIn SQRT ! take root to get rms of square fluctuation data.
SCALar WMAIn SHOW SELE TYPE CB END ! show the results for each residue
Note: to get the mass weighted average rms fluctuations, remove steps 3 and 5.
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory