1,330
edits
Reflection files format: Difference between revisions
Jump to navigation
Jump to search
→LCF
(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...") |
(→LCF) |
||
| (8 intermediate revisions by the same user not shown) | |||
| Line 197: | Line 197: | ||
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: | |||
<pre> | |||
! 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: | |||
! ifort lcf_dump.f90 -o lcf_dump | |||
IMPLICIT NONE | |||
! LCF items | |||
INTEGER(2) :: header(8),ncol | |||
INTEGER(2), ALLOCATABLE :: refdat(:) | |||
REAL :: cell(6) | |||
CHARACTER :: separator*12 ! length may depend on machine that wrote LCF file | |||
! program variables | |||
INTEGER :: i | |||
CHARACTER :: string*120 | |||
i=COMMAND_ARGUMENT_COUNT() | |||
IF (i/=1) STOP 'usage: lcf_dump <name.LCF>' | |||
! 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) | |||
! read header and cell | |||
READ(1) header,separator ! reads 8*2+12 bytes. ends after byte 28 | |||
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 | |||
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,(header(8)+3)/4 | |||
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> | |||