CP FROM PDB - Copy PDB file to SPIDER format

(06/05/13)

PURPOSE

Copy a PDB image data file to SPIDER volume.   Example.

SEE ALSO

CP FROM ASCII [Copy ASCII text file to SPIDER file]
CP FROM EMI [Copy EMISPEC format file to SPIDER file]
CP FROM MRC [Copy MRC file to SPIDER file]
CP FROM NIK [Copy Nikon Coolscan format file to SPIDER file]
CP FROM PDB [Copy PDB file to SPIDER format]
CP FROM RAW [Copy Raw Image to SPIDER file]
CP FROM TERM [Copy Terminal input to SPIDER image/volume]
CP FROM TIFF [Copy TIFF format file to SPIDER file]
CP FROM VAX [Copy VAX SPIDER file to a Unix SPIDER file]
CP TO ASCII [Copy SPIDER file to ASCII text format]
CP TO BRIX [Copy SPIDER volume to BRIX file for "O" input]
CP TO MRC [Copy SPIDER file To MRC (CCP4) format file]
CP TO OPEND [Copy SPIDER file To Opposite Byte Endian]
CP TO POST [Copy SPIDER image to a POSTscript image]
CP TO RAW [Copy SPIDER file to a 8-bit raw image]
CP TO TIFF [Copy SPIDER file to a TIFF format]

USAGE

.OPERATION: CP FROM PDB

.PDB INPUT FILE: TRNA03.PDB
[Enter the name of the PDB file including extension.]

.VOXEL SIZE [A]: 2.2
[Enter the voxel size of SPIDER file in Angstroms.]

.CENTER? (Y/N): Y
[Do you want the PDB file to be centered within the SPIDER volume? If No, the PDB file will be placed in the "absolute" location, as defined by atomic coordinates given.
If Yes, the average X, Y, Z coordinates will coincide with the center of SPIDER volume ( INT(NX/2)+1)....]

.ATOMS OR TEMPERATURE? (A/T): A
[Do you want SPIDER volume to contain an Atoms/Occupancy value or a 'Temperature' value?]

.SPIDER VOLUME SIZE, NX, NY, & NZ: 75, 89, 85
[Enter size of the SPIDER file (number of voxels in each dimension). SPIDER reports the minimum acceptable size adjusted for centering prior to this question.]

.SPIDER OUTPUT FILE: TRNA03
[Enter name for the file that will contain the volume.]

NOTES

  1. The program reads atomic coordinates of a structure from a PDB file, then creates a SPIDER volume by adding the Z values times the occupancy factor in each resolution cell. The density is proportional to the Coulomb potential.

  2. The SPIDER coordinate system differs from that used in PDB files.

SUBROUTINES

READPDB

CALLER

COPY1

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