STEREO (CCP4: Supported Program)

NAME

stereo - Extract coordinates from stereo diagrams

SYNOPSIS

stereo xyzin coordinate_file xyzout coord.brk
[Keyworded input]

DESCRIPTION

The stereo program recreates three-dimensional coordinates on the basis of a pair of two-dimensional ones extracted from a stereo diagram. The input coordinates are taken from the logical name XYZIN (see FORMAT OF XYZIN) into a PDB-format file on XYZOUT. The output will not necessarily be a sensible PDB file, especially if the optional information about atom names and residue types isn't supplied. The programs coordconv, reform, and pdbset may be useful for manipulating the output.

The input coordinates are expected to be measured (from some publication for which you don't have the coordinates electronically) with a flatbed cross-hair digitiser or similar device. If you don't have such a device you might be able to do this:

make a transparency of the picture;
stick it against a graphics screen and fire up some drawing program from which you can get the data in a sensible form, e.g. `xfig';
draw points or lines to trace each stereo view and save the drawing;
mangle the drawn points output into a suitable form for input to this program (see below) using your favourite utility.

KEYWORDED INPUT

Available keywords are:

CRITERION, CONSTRAINT, PHI, TITLE, VIEWSET.

TITLE <title>

PHI <phi>

Angular separation of the stereo components in degrees. If not given the correct value will be searched for.

VIEWSET <v>

Viewing distance in inches. If not given the correct value will be searched for.

CRITERION <crit>

Criterion for removing bad measurements from <phi> and <v> searches. The default value is 1.5. Prior to <phi>, <v> search, the program uses <phi>=3 degrees, <v>=infinity, and distances used in constraints. All distances which are outside the range (s*<crit>,s/(<crit>**2)), where s is the standard Ca-Ca distance of 3.84 A, will be rejected from the search.

CONSTRAINT <const1> <const2> <const3> <const4>

Specify a constraint. If no constraints are specified a polypeptide chain of alpha carbon atoms will be assumed and the distances between succeeding pairs of atoms will be refined against the standard alpha carbon - alpha carbon distance of 3.84 Angstroms.

<const1>: First i-th atom in constraint
<const2>: First j-th atom in constraint (if negative, will count backwards).
<const3>: Last i-th atom in constraint
<const4>: Distance s(i,j) between i-th and j-th atoms measured in Angstroems.

If <const2>=0 for the k-th constraint line, an alpha helix is assumed. In this case <const1> should be the first carbon alpha atom in the helix (call it atom i) and <const3> should be the last carbon alpha atom in the helix (call it atom j) and a series of constraints is generated in place of the given constraint as follows.

The first set of constraints will be for

atom i to atom i+2
atom i+1 to atom i+3                                           
etc. until i+n=j

The second set of constraints will be for

atom i to atom i+3                                             
atom i+1 to atom i+4                                           
etc. until i+n=j                                               
the last constraint will be for                                    
atom i to atom j

By assuming the parameters for an alpha helix, the program works out the appropriate values for s(i,j) in subroutine HELIX.

Examples of particular constraints that may be set are

An alpha carbon chain of n atoms.
CONSTRAINT 1 2 n-1 3.84
Two antiparallel strands, each n residues long, starting at residue numbers p and q.
CONSTRAINT p -(q+n-1) (p+n-1) 4.72 (Note: there are two different Ca-Ca distances between antiparallel strands and this number is an average.)
An alpha helix n residues long starting at residue p.
CONSTRAINT p p+4 p+n-4 6.20

The program will minimise the sum over all the constraints of
sum(((x(i)-x(j))**2-s(i,j)**2)**2)

FORMAT OF XYZIN

The input data file comprises free format records of the form
<xl> <yl> <xr> <yr> [ <atom name> [ <residue name> [ <residue number>] ] ]

These are the left and right stereo diagram coordinates. It is assumed that the coordinates will be given in microns, so as to provide the viewing distance in inches. The program will work if the coordinates are in any other units but the <v> distance will not be in inches but on a corresponding arbitrary scale. Each coordinate has an optional <atom name>, <residue name> and <residue number> which will be used in he XYZOUT file if given. Otherwise dummy tags will be used.

STANDARD OUTPUT

The output is hopefully self explanatory but essentially it consists of the following sequential items following header.

Echo of input data
Refinement of orientation of x,y coordinates to minimise y separation in left and right equivalent atoms.
x and y refined to separate origins.
Statistics on separation of x and y coordinates. initial determination of <phi>.
Search for best <phi> and <v>.
Best value of <phi> and <v>.

x, y, z three-dimensional coordinates for each cycle of refinement.

          a. 3 cycles of z refinement                                     
          b. 3 cycles of y refinement                                     
          c. 3 cycles of x refinement

Shifts (in Angstroms), coordinates and rms for each constraint are given after each cycle.

AUTHOR

M. G. Rossmann                             March 1979 
        Dept. of Biological Sciences                                      
        Purdue University                                                 
        West Lafayette, Indiana 47907                                     

Modified and reorganized with new math routines
        b4x@mace.cc.purdue.edu         August 5, 1994

Hacked into CCP4 conventions (basically i/o) at Daresbury.