NAME

arctransform - convert an archive record using rigid body transformations

SYNOPSIS

arctransform [ options ] -i arcfile1 -o arcfile2

DESCRIPTION

Read the first record of the binary archive file arcfile1, transform it and write the modified record to the binary archive file arcfile2. Only the first record is converted and written to the output and the first record must contain a coordinate set. If there are velocities they are copied to the output archive verbatim. arcfile1 must exist and arcfile2 must not.

The transforms are read from the standard input. The transforms are specified as a series of rotation matrices and displacement vectors. See the FILE section for the format of this file.

If options are specified, the standard input is ignored. The options are:

-center: Re-center the coordinates. The coordinates are moved so that the centroid is at the origin (0,0,0). If specified, this transform is applied first.

-scale S: Scale the coordinates uniformly by the factor S. If specified, this transform is applied next. Negative scales are allowed. A zero scale is allowed but this will squeeze the model back to its state before the Big Bang.

-shift a b c: Move the entire coordinate set by aÅ along the x-axis, bÅ along the y-axis and cÅ along the z-axis.

-theta H: Rotate the entire coordinate set about the first axis by H degrees.

-phi F: Rotate the entire coordinate set about the second axis by F degrees.

-omega W: Rotate the entire coordinate set about the third axis by W degrees.

The allowable values of angles are from -180 to +180 degrees. The rotations are applied about the first axis, then about the rotated second axis and finally about the rotated third axis. If you want a rotation about only one axis, you only need to specify one angle. Note that these are not Euler angles.

The shifts and rotations are applied together.

EXAMPLE

arctransform -shift 1.5 -2 0 -i test.ar -o out.ar

Shift the coordinates in test.ar 1.5Å along the x-axis and -2Å along the y-axis and write the modified coordinates to out.ar.

arctransform -i test.ar -o out.ar < xform

Apply the transformation in the file xform to test.ar and write the modified coordinates to out.ar.

FILES

The transform file is a text file which should be extracted from the standard output of Yammp. Each transformation starts with a line that begins with the words "Rigid Unit", the rest of the line is ignored. Following the header line is the description of the first rigid unit. The atom numbers are enclosed by braces. Three lines follow the rigid unit description. The elements of the rotation matrix and the displacement vector are listed in these three lines. The second rigid unit is listed next and so on. If there are more transformations, list them following the same pattern starting with the header line.

The rotation matrices must be orthonormal or the model will be distorted.

Rigid Unit {Atom Range}: ( Rotation ) [ Translation ]
1	{	Atomfirst	Atomlast	}:
	(	R1,1	R1,2	R1,3	)	[	dx	]
	(	R2,1	R2,2	R2,3	)	[	dy	]
	(	R3,1	R3,2	R3,3	)	[	dz	]
...	{	...	...	}
	(	...	...	...	)	[	...	]
Rigid Unit the rest of this line is ignored
1	{	...	...	}:
	(	...	...	...	)	[	...	]

It is best to cut the transform file from the output of Yammp. Cut out extraneous text and blank lines and do not change the lines that matter in any way.

One purpose of this utility is to apply the transformations derived from one model (usually a reduced representation model) to another (perhaps an all-atom model). The only items that will change will be atom numbers. Be sure to observe the rules: numbers must be within the range of 1 to the total number of atoms in the model, the first atom number must be less than or equal to the last atom number in each rigid unit, atom ranges do not overlap and the atom numbers increases with each additional rigid unit. Remember to change the atom ranges for all units and for all transformations. The atom ranges for a given unit must be the same in all transformations.

SEE ALSO

DIAGNOSTICS

BUGS

NOTES

 This utility is not currently part of the public distribution.