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In this example, we prepare an image which has 9 pictures generated from time points in a molecular dynamics calculation of McPC 603. Only the hypervariable loops are displayed and the loop are color coded so that they can be distinguished.
Display of 9 images of hypervariable loops of McPC 603
*
OPEN NAME CGDATA:RTOPH8.MOD UNIT 01 READ UNFORM
OPEN NAME CGDATA:PARAM5.MOD UNIT 03 READ UNFORM
OPEN NAME [BRUC.SEARCH]M603VPSF.MOD UNIT 12 READ UNFORM
OPEN NAME [BRUC.M603.A.NEW]M6VAMN18.MOD UNIT 14 READ UNFORM
READ RTF UNIT 1
READ PARAMETER UNIT 3
READ PSF FILE UNIT 12
READ COOR FILE UNIT 14
!
! At this point, everything we need except the trajectory has been read.
! We now orient the coordinates to a standard orientation.
!
COOR ORIENT CLEAR ATOM H 22 CA ATOM H 98 CA ATOM L 23 CA ATOM L 94 CA
OPEN UNIT 20 NAME MCPDYN.IMG WRITE UNFORM ! File where image will go
SPHERE
TL ; McPC 603 DYNAMICS, 500 K. 0,6,12,20,34,54,74,94,114 PS;
!
! Display only the hypervariable loops.
!
RM ALL
AD CLEAR RANGE H 31 N H 35 O -
RANGE H 51 N H 65 O -
RANGE H 101 N H 107 O -
RANGE L 24 N L 40 O -
RANGE L 56 N L 62 O -
RANGE L 95 N L 103 O
AS 3.2 ! Need three fold reduction
YR 180 ! Reorient for better view.
CO 1 CLEAR RANGE H 31 N H 35 O ! Color the loops
CO 2 CLEAR RANGE H 51 N H 65 O
CO 3 CLEAR RANGE H 101 N H 107 O
CO 2 CLEAR RANGE L 24 N L 40 O
CO 1 CLEAR RANGE L 56 N L 62 O
CO 4 CLEAR RANGE L 95 N L 103 O
OC -4.3 3.8 ! First picture in top left
TR ! Make spheres for first picture
EX ! Back to CONGEN for more work
OPEN UNIT 14 NAME D18.CRD UNFORM READ ! Trajectory
READ COOR FILE UNIT 14 IFILE 30 ! Get fresh coordinates
!
! Reorient like the first set
!
COOR ORIENT CLEAR ATOM H 22 CA ATOM H 98 CA ATOM L 23 CA ATOM L 94 CA
SPHERE
OC 4 0 ! Second picture to right of first.
TR ! Add spheres for next picture. The
! previous transformation applies.
EX
!
! Spheres for the next seven pictures are generated the same way.
!
OPEN UNIT 14 NAME D18.CRD UNFORM READ
READ COOR FILE UNIT 14 IFILE 60
COOR ORIENT CLEAR ATOM H 22 CA ATOM H 98 CA ATOM L 23 CA ATOM L 94 CA
SPHERE
OC 4 0 ! Third picture to right of second.
TR
EX
OPEN UNIT 14 NAME D18.CRD UNFORM READ
READ COOR FILE UNIT 14 IFILE 100
COOR ORIENT CLEAR ATOM H 22 CA ATOM H 98 CA ATOM L 23 CA ATOM L 94 CA
SPHERE
OC -8 -3.7 ! Fourth picture at middle left
TR
EX
OPEN UNIT 14 NAME D18.CRD UNFORM READ
READ COOR FILE UNIT 14 IFILE 170
COOR ORIENT CLEAR ATOM H 22 CA ATOM H 98 CA ATOM L 23 CA ATOM L 94 CA
SPHERE
OC 4 0 ! Fifth picture at center.
TR
EX
OPEN UNIT 14 NAME D18.CRD UNFORM READ
READ COOR FILE UNIT 14 IFILE 270
COOR ORIENT CLEAR ATOM H 22 CA ATOM H 98 CA ATOM L 23 CA ATOM L 94 CA
SPHERE
OC 4 0 ! Sixth picture at center right
TR
EX
OPEN UNIT 14 NAME D18.CRD UNFORM READ
READ COOR FILE UNIT 14 IFILE 370
COOR ORIENT CLEAR ATOM H 22 CA ATOM H 98 CA ATOM L 23 CA ATOM L 94 CA
SPHERE
OC -8 -3.7 ! Seventh picture at bottom left
TR
EX
OPEN UNIT 14 NAME D18.CRD UNFORM READ
READ COOR FILE UNIT 14 IFILE 470
COOR ORIENT CLEAR ATOM H 22 CA ATOM H 98 CA ATOM L 23 CA ATOM L 94 CA
SPHERE
OC 4 0 ! Eighth picture at bottom center
TR
EX
OPEN UNIT 14 NAME D18.CRD UNFORM READ
READ COOR FILE UNIT 14 IFILE 570
COOR ORIENT CLEAR ATOM H 22 CA ATOM H 98 CA ATOM L 23 CA ATOM L 94 CA
SPHERE
OC 4 0 ! Ninth picture at bottom right
TR
EX
SPHERE
IM ! Finally, construct the image from
! all the spheres we've collected.
WI 20 ! Write the image out
EX ! All done.