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CP TO BRIX - CoPy SPIDER volume to BRIX file for O input

(10/10/96)

PURPOSE

Copies a SPIDER-format volume file into a "Brix" file file compatible with the MAP_FILE option of the "O" molecular modeling program. In O, MAP_DRAW produces a wiremesh representation that can be moved interactively using knob controls. Several objects imported from SPIDER can thus be moved independently.

SEE ALSO

CP FROM ASCII [CoPy FROM ASCII text file to Spider file]
CP FROM JP [CoPy FROM JP file to Spider file]
CP FROM MRC [CoPy FROM MRC files to Spider files]
CP FROM PDB [CoPy FROM PDB file to Spider file]
CP FROM RAW [CoPy FROM RAW image to Spider file]
CP FROM SF3 [CoPy FROM Simple file to 3D Fourier file]
CP FROM SHORT [CoPy FROM SHORT-label file to Spider standard file]
CP FROM TERM [CoPy FROM TERMinal to Spider file]
CP FROM VAX [CoPy FROM VAX to Unix file]
CP FROM VAX16 [CoPy FROM VAX to 16-bit Unix file]
CP TO ASCII [CoPy TO ASCII text file from Spider file]
CP TO BRIX [CoPy TO pre-BRIX file from Spider file]
CP TO MRC [CoPy TO MRC files from Spider files]
CP TO POST [CoPy TO POSTscript format from Spider file]
CP TO RAW [CoPy TO RAW 8-bit Unix file from Spider file]
CP TO SF3 [CoPy TO simple format from 3D Spider Fourier file]
CP TO SGI [CoPy TO SGI format from Spider file]
CP TO TARGA [CoPy TO TARGA format file from Spider file]
CP TO TARGAV [CoPy TO TARGA format from VAX file [on SGI only]]
CP TO TIFF [CoPy TO TIFF file from Spider file]
CP TO VAX [CoPy TO VAX file from Unix file]
CP TO VV [CoPy TO Voxel_View files from Spider Unix 3D volume]

USAGE

.OPERATION: CP TO BRIX

.SPIDER INPUT FILE: VOL001
[Enter the name of the SPIDER file containing the volume. Make sure the volume has valid FMIN, FMAX, e.g. from a previous display by WEB, or operation 'FS']

.OUTPUT FILE: VOL001.PREBRIX
[Enter the name of the map file (formatted for input to map_file option of O) into which you want to copy the volume. Use complete file name (incl. any extension). Extension will not be overwritten.]

.SAMPLING DISTANCE: 5.2
[Enter the sampling distance, in Angstrom]

.DEFAULT UNIT CELL IS NSAM,NROW,NSLICE. OVERWRITE (Y/N)? Y
[Enter 'Y' if you wish to overwrite the default dimensions given by the dimensions of the volume. Note that the fictitious orthogonal unit cell dimensions are merely used for setting up display parameters.]

If you have selected 'Y' as in above example:

.ENTER UNIT CELL DIMS (X,Y,Z): 80,60,60
[Enter the cell dimensions]

If you have not selected 'Y':

No further input is solicited, and the volume dimensions are taken as unit cell dimensions.

NOTES

  1. The origin of the "unit cell" is set at -NSAM/2, -NROW/2, -NSLICE/2.

  2. Upon reading in the map file, O restores the original density range of the data based on the values of scale and offset parameters stored in the file's header. Because of format limitations of O, scale and offset will not be read correctly unless the SPIDER file has a density range specified in one or two digits before the decimal point. Therefore 'AR' (followed by 'FS') should be used in SPIDER to multiply the volume prior to 'CP BRIX' so that the density is pushed into a "safe" range.

  3. J. Frank 4/10/95

SUBROUTINES

COPYBRIX

CALLER

COPY1

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