26.1.4 Transformations from the Coordinates to the Image

The commands for controlling the transformation from atomic coordinates to the spheres list are described below. They take effect for any TR commands executed thereafter.

26.1.4.1 AS — Automatic Scaling

Syntax:

AS real

Function:

Automatic scaling. The purpose of automatic scaling is to set transformation parameters so that the image will be centered in the Deanza screen and make full use of the screen. Both the scale factor and the origin shifts (OC) are set. In addition, the rotation origin (the point about which the rotation matrix is applied) is set to midpoint of the molecule. If a real number is specified, it is used to scale down the size of the image so that it will less of the screen. E.g., a scale factor of 2 will result in a image that whose maximum vertical or horizontal dimension will be less than half the screen.

26.1.4.2 DV — Set Device Drawing Parameters

Syntax:

DV string

Function:

Device setting. This command will set the number of pixels in the vertical and horizontal dimensions as well as the screen size according to the device you specify by the string. The following devices are recognized:

          Device name   Xpixels   Ypixels  Xscreen  Yscreen
          
          IRIS or 4D      1250      994     33.75    26.84
          PS390           1024      864     32.5     27.42
          DEANZA           512      512     20.0     20.00
          DUMMY             25       25      1.0      1.0
     

If the device name is not recognized, then the DEANZA dimensions are used.

26.1.4.3 HOME — Reset Sphere Drawing Parameters

Syntax:

HOme

Function:

Initialize everything to starting state. I.e. origin shifts are set to zero, the rotation matrix is set to the identity matrix, scale factor is set to 1 Angstrom for the screen size, colors back to their default, etc.

26.1.4.4 IR — Input Rotation Matrix

Syntax:

IR real real real real real real real real real

Function:

Input rotation matrix. The elements are read in the following subscript order, 11 12 13 21 22 23 31 32 33.

26.1.4.5 OC — Shift Screen Origin in Centimeters

Syntax:

OC real real real

Function:

Origin shift in centimeters. The image is moved relative to the screen in units of centimeters by the amounts given in the command. The first number gives the horizontal shift; the second number gives the vertical shift; the third the depth shift, which will be significant if two separate images are overlaid upon each other.

26.1.4.6 OD — Set Origin of Data

Syntax:

OD real real real

Function:

Set Origin of Data, ie. origin of rotation. The rotation matrix will be applied about this origin. The origin is specified by X, Y, and Z in the space of atomic coordinates.

26.1.4.7 OR — Set Origin of Data in Screen Size Units

Syntax:

OR real real real

Function:

Set the picture origin in units of the screen size. The three arguments give the X, Y, and Z; horizontal, vertical, and depth shifts; respectively. Upon initialization, the origin is set at the bottom left of the screen. This command moves the origin so that image is shifted by the amounts specified in the command. For example, if the atomic coordinates are centered about the origin, an OR 0.5 0.5 command will center the image about the center of the screen. An OR 1.0 command will center the image about the lower right corner of the screen. The Z shift can be useful to control how two different molecules will overlay each other. This command works by changing the OC parameters described above.

26.1.4.8 SA — Scale in Angstrom Units

Syntax:

SA real

Function:

Sets the scale factor which is in units of Angstroms / cm. For example, SA 2 will set a scale factor of 2 Angstroms/cm. The actual size of a centimeter on the screen depends on the device parameters which specify the number of pixels and screen size in each dimension. If the argument is omitted, the scale factor will be set to 1.

26.1.4.9 SCALE — Scale by a Multiplicative Factor

Syntax:

SCale real

Function:

Multiplies the current scale factor by the argument to this command. If the argument is not specified, the command has no effect.

26.1.4.10 SHOW, SR — Show Drawing Parameters

Syntax:

SHow

Function:

Show Rotation and other transformation parameters. Prints the rotation matrix, data origin (OD), origin shift (OC), scale factor (SA), and a checksum for the image.

Syntax:

SR

Function:

Same as SH above.

26.1.4.11 SO — Set Stereo Offset

Syntax:

SO real real

Function:

Stereo Offset command. The first argument specified the rotation in degrees about the Y axis to be applied. The second argument moves the image that many centimeters to the right. A typical command here would be SO 6 6.

26.1.4.12 XP — Set Horizontal (X) Pixel Count

Syntax:

XP int

Function:

Sets the number of pixels in the horizontal (X) dimension.

26.1.4.13 XR — X Rotation

Syntax:

XR real

Function:

Rotation about X axis. The argument specifies how degrees about the X axis the image should be rotated. The command results in the modification of the rotation matrix.

26.1.4.14 XS — Set Horizontal (X) Screen Size

Syntax:

XS real

Function:

Sets the screen size in centimeters for the horizontal (X) dimension. N.B. Be careful to avoid a difference between the number of pixels per centimeter in the horizontal and vertical dimensions unless you are trying to generate some unusual visual effects.

26.1.4.15 YP — Set Vertical (Y) Pixel Count

Syntax:

YP int

Function:

Sets the number of pixels in the vertical (Y) dimension.

26.1.4.16 YR — Y Rotation

Syntax:

YR real

Function:

Rotation about Y axis. The argument specifies how degrees about the Y axis the image should be rotated. The command results in the modification of the rotation matrix.

26.1.4.17 YS — Set Vertical (Y) Screen Size

Syntax:

YS real

Function:

Sets the screen size in centimeters for the vertical (Y) dimension. N.B. Be careful to avoid a difference between the number of pixels per centimeter in the horizontal and vertical dimensions unless you are trying to generate some unusual visual effects.

26.1.4.18 ZCUT — Mark Atoms by Transformed Z's

Syntax:

ZCUT real

Function:

ZCUT defines a visibility plane normal to the Z axis. Only those atoms whose upper surface is less than the parameter specified to this command will be displayed. The determination of Z is made after the molecule has been rotated. See the ZMARK command, Atom Manipulations in Sphere Drawing, for a variant.

26.1.4.19 ZR — Z Rotation

Syntax:

ZR real

Function:

Rotation about Z axis. The argument specifies how degrees about the Z axis the image should be rotated. The command results in the modification of the rotation matrix.