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Reflection files format: Difference between revisions
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The CCP4 LCF (labelled column format) files were phased-out in the early 90's but some interesting data still lingers on half-inch tapes so, if they can be read, the LCF files can be converted to ASCII or other formats for safe-keeping, or further use. | The CCP4 LCF (labelled column format) files were phased-out in the early 90's but some interesting data still lingers on half-inch tapes so, if they can be read, the LCF files can be converted to ASCII or other formats for safe-keeping, or further use. | ||
Jonathan Cooper has worked out how to read them, mainly using Python, and [https://readingccp4lcffiles.blogspot.com/ documents this]. | Jonathan Cooper has worked out how to read them, mainly using Python, and [https://readingccp4lcffiles.blogspot.com/ documents this]. The directory ftp://ftp.ccp4.ac.uk/lcfstuff/ has some Fortran routines. | ||
A Fortran program (lcf_dump) to accomplish this is: | A Fortran program (lcf_dump) to accomplish this is: | ||
<pre> | <pre> | ||
! reads cell from LCF file - Kay Diederichs 7/2019 . | ! reads cell, column labels, comment, and reflection data from LCF file - Kay Diederichs 7/2019 . | ||
! | ! Nota bene - symmetry i.e. space group seemingly not stored in LCF file | ||
! reading VAX format is easy with the ifort compiler since it understands VAX REAL format: | ! reading VAX format is easy with the ifort compiler since it understands VAX REAL format: | ||
! ifort lcf_dump.f90 -o lcf_dump | ! ifort lcf_dump.f90 -o lcf_dump | ||
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! LCF items | ! LCF items | ||
INTEGER(2) :: header(8) | INTEGER(2) :: header(8),ncol | ||
INTEGER(2), ALLOCATABLE :: refdat(:) | INTEGER(2), ALLOCATABLE :: refdat(:) | ||
REAL :: cell(6) | REAL :: cell(6) | ||
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! program variables | ! program variables | ||
INTEGER :: i | INTEGER :: i | ||
CHARACTER :: string*120 | CHARACTER :: string*120 | ||
i=COMMAND_ARGUMENT_COUNT() | i=COMMAND_ARGUMENT_COUNT() | ||
IF (i/= | IF (i/=1) STOP 'usage: lcf_dump <name.LCF>' | ||
! read command line | ! read command line | ||
CALL GET_COMMAND_ARGUMENT(1,string) ! expects LCF filename on command line | CALL GET_COMMAND_ARGUMENT(1,string) ! expects LCF filename on command line | ||
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OPEN(1,FILE=string,ACCESS='STREAM',ACTION='READ',CONVERT='VAXG') | OPEN(1,FILE=string,ACCESS='STREAM',ACTION='READ',CONVERT='VAXG') | ||
WRITE(*,*) 'LCF file: ',TRIM(string) | WRITE(*,*) 'LCF file: ',TRIM(string) | ||
! read header and cell | ! read header and cell | ||
READ(1) header,separator ! reads 8*2+12 bytes. ends after byte 28 | READ(1) header,separator ! reads 8*2+12 bytes. ends after byte 28 | ||
WRITE(*,'(a,8(i0,1x))') ' header: ',header | WRITE(*,'(a,8(i0,1x))') ' header: ',header | ||
! the following code determines ncol according to lcflib.f line 1534ff: | |||
IF (header(1) /= -32768) STOP 'error - first header item is not -32768' | |||
IF (header(5) == -12) THEN | |||
ncol=6 | |||
ELSE IF (header(6)==-14) THEN | |||
ncol=7 | |||
ELSE | |||
ncol=-header(7)/2 | |||
IF (ncol<0 .OR. ncol>100) STOP 'error - could not determine ncol' | |||
END IF | |||
WRITE(*,'(a,i0)') ' ncol: ',ncol | |||
ALLOCATE(refdat(ncol)) | |||
DO i=1,6 | DO i=1,6 | ||
READ(1) cell(i),separator ! reads 6*(4+12) bytes. ends after byte 124 | READ(1) cell(i),separator ! reads 6*(4+12) bytes. ends after byte 124 | ||
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! read column labels and comment | ! read column labels and comment | ||
string='' | string='' | ||
DO i=1,( | DO i=1,(header(8)+3)/4 | ||
READ(1)string(1+(i-1)*4:i*4),separator | READ(1)string(1+(i-1)*4:i*4),separator | ||
END DO | END DO | ||