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Reflection files format: Difference between revisions
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(Created page with "CCP4 reflection files are binary files that are usually read by routines from CCP4 libraries. However, sometimes one wants to read them with a different programming language o...") |
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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]. | ||
A Fortran program (lcf_dump) to accomplish this is: | |||
<pre> | |||
! reads cell from LCF file - Kay Diederichs 7/2019 . | |||
! TODO - determine ncol, offset from data in file | |||
! reading VAX format is easy with the ifort compiler since it understands VAX REAL format: | |||
! ifort lcf_dump.f90 -o lcf_dump | |||
IMPLICIT NONE | |||
! LCF items | |||
INTEGER(2) :: header(8) | |||
INTEGER(2), ALLOCATABLE :: refdat(:) | |||
REAL :: cell(6) | |||
CHARACTER :: separator*12 ! length may depend on machine that wrote LCF file | |||
! program variables | |||
INTEGER :: i,ncol,offset | |||
CHARACTER :: string*120 | |||
i=COMMAND_ARGUMENT_COUNT() | |||
IF (i/=3) STOP 'usage: lcf_dump <name.LCF> ncol offset' | |||
! read command line | |||
CALL GET_COMMAND_ARGUMENT(1,string) ! expects LCF filename on command line | |||
! OPEN(CONVERT=...) options are documented at | |||
! https://software.intel.com/en-us/fortran-compiler-developer-guide-and-reference-open-convert-specifier | |||
OPEN(1,FILE=string,ACCESS='STREAM',ACTION='READ',CONVERT='VAXG') | |||
WRITE(*,*) 'LCF file: ',TRIM(string) | |||
CALL GET_COMMAND_ARGUMENT(2,string) ! expects NCOL | |||
READ(string,*) ncol | |||
ALLOCATE(refdat(ncol)) | |||
CALL GET_COMMAND_ARGUMENT(3,string) ! expects NCOL | |||
READ(string,*) offset | |||
WRITE(*,*) 'ncol, offset:',ncol,offset | |||
! read header and cell | |||
READ(1) header,separator ! reads 8*2+12 bytes. ends after byte 28 | |||
WRITE(*,'(a,8(i0,1x))') ' header: ',header | |||
DO i=1,6 | |||
READ(1) cell(i),separator ! reads 6*(4+12) bytes. ends after byte 124 | |||
END DO | |||
WRITE(*,'(a,6f10.4)') ' cell:',cell | |||
! read column labels and comment | |||
string='' | |||
DO i=1,22 | |||
READ(1)string(1+(i-1)*4:i*4),separator | |||
END DO | |||
WRITE(*,'(a)') TRIM(string) | |||
! read reflections | |||
READ(1) refdat(1:2) ! needed for positioning - what is their meaning? | |||
DO | |||
READ(1) refdat | |||
IF (refdat(1)==32767) EXIT | |||
WRITE(*,*) refdat | |||
END DO | |||
END | |||
</pre> | |||