Collaborative Computational Project No. 4
Software for Macromolecular X-Ray Crystallography

Known Problems with ccp4 4.1.x

These are the known problems with release 4.1 of the CCP4 suite, together with fixes where appropriate. Code changes are given as patches, which can be applied with the UNIX patch utility. New files are put in the prerelease directory, which can be found at ftp://ccp4a.dl.ac.uk/ccp4/prerelease. And there is some more info on what the files are.

Hints and advice about applying the fixes can be found here.

Problems with current releases

General and system specific problems

A list of more general version-unspecific problems can be found The General Problems Page lists general version-unspecific problems as well as descriptions of various operating system-specific eccentricities.

Warning for Linux users: if you are running CCP4 compiled with gcc 2.96 may be unreliable.. This has been seen with RedHat 7.0 and Mandrake 8.1.

A list of general problems with CCP4i can be found here.

Problems with MOSFLM

As of CCP4 4.1, MOSFLM is released as part of the CCP4 program suite; for problems on MOSFLM please refer to Harry Powell's MOSFLM page:

Older versions of CCP4

Older versions of the suite are not supported. The first step in attempting to solve a problem in older versions should be to upgrade to the current release. However, problems and fixes for older versions can be found here: Note that these pages are also unsupported and will most probably be out of date - particularly references to prerelease files.

Problems with 4.1.1


Installation


1. Long compilation times for Mosflm on IRIX64. Date : 15/3/2001.

Under IRIX64 mosflm may take a considerable amount of time to compile, 600+ minutes. This is due to the setting of Olimit=0 (some cases only) which optimises all routines, regardless of length.

The solution is to set the Olimit values in the configure script to a sensible value (1500 is used in most cases).

 diff -C1 -c -r1.126 -r1.127
*** configure   2001/01/31 14:41:52     1.126
--- configure   2001/03/15 10:01:27     1.127
***************
*** 745,747 ****
      IRIX64\ 6.5*|IRIX\ 6.5*)
!       XFFLAGS=${XFFLAGS-"-64 -mips3 -nocpp -OPT:Olimit=0 -w"}
        XCFLAGS=${XCFLAGS-"-64 -DPROTOTYPE -w"}
--- 745,747 ----
      IRIX64\ 6.5*|IRIX\ 6.5*)
!       XFFLAGS=${XFFLAGS-"-64 -mips3 -nocpp -OPT:Olimit=1500 -w"}
        XCFLAGS=${XCFLAGS-"-64 -DPROTOTYPE -w"}
***************
*** 755,757 ****
      *)
!       XFFLAGS=${XFFLAGS-"-64 -mips3 -nocpp -OPT:Olimit=0 -w"}
        XCFLAGS=${XCFLAGS-"-64 -DPROTOTYPE -w"}
--- 755,757 ----
      *)
!       XFFLAGS=${XFFLAGS-"-64 -mips3 -nocpp -OPT:Olimit=1500 -w"}
        XCFLAGS=${XCFLAGS-"-64 -DPROTOTYPE -w"}
***************
*** 781,783 ****
    IRIX64*)
!     XFFLAGS=${XFFLAGS-"-OPT:Olimit=1500 1500  -nocpp"}
  #    XLDFLAGS=${XLDFLAGS-"-lfpe"} # to enable floating point traps
--- 781,783 ----
    IRIX64*)
!     XFFLAGS=${XFFLAGS-"-OPT:Olimit=1500 -nocpp"}
  #    XLDFLAGS=${XLDFLAGS-"-lfpe"} # to enable floating point traps

Alternatively config.status may be similarly edited.

(Thanks to Robert Campbell for spotting this)


2. newly created file is older than distributed files! Date : 16/3/2001.

Under certain circumstances the configure script in xdl_view will fail with:

configure: error: newly created file is older than distributed files!
Check your system clock

This occurs when the filesystem with ccp4 is mounted on a remote machine, and the remote machine's clock is slower than the local machine's. A solution is, for the configure script in xdl_view:

diff -c -C1 configure configure_new
*** configure   Thu Jan 18 09:33:26 2001
--- configure_new       Fri Mar 16 11:40:23 2001
***************
*** 971,972 ****
--- 971,973 ----
  echo timestamp > conftestfile
+ touch conftestfile
  # Do `set' in a subshell so we don't clobber the current shell's

(Thanks to Randy Read for the suggestion)


Programs


1. AMORE.
Date : 6/3/2001.

There is a bug in Amore which shows itself only when the search is in a monoclinic space group where b is shorter than c. Thanks all those who pointed the error out (and Eleanor for fixing it!).

Please download and install a fixed amore.f from the prerelease area.
Problem symptom is a program exit of the following nature:

 > S/R PAC4 < MAXIMAL INDICES EXCEEDED:
  Indices are:   6 -52   0   Limits are:  83  48 106 Adding: 168 100 216
 Number of symmetry equivalent:   2 Limit is:  5
 Generated Packed number ( should be > 0..)             890108
 AMORE:   > s/r pac4 < maximal indices exceeded:

(Thanks to Eleanor Dodson for the changes.)


2. REFMAC5 - loggraphs.
Date : 15/3/2001
Updated : 29/3/2001

An error in the refmac5 output means that some graphs fail to display in (x)loggraph.

Please download and install fixed versions of the subag_scale.f and refmac_newdic.f files from the prerelease area. NB: these two files should be put into the $CPROG/refmac5_ directory.


3. REFMAC5
Date: 20/03/2001

If you are using REFMAC5 and you have residues like NAD, NDP, FAD etc then the program may stop with the message:

No match for full atom ID - subtract one character
It is related to the fact that REFMAC5 cannot extract element names for these atoms. The solution is to add element names for these residues.

Garib Murshudov has written a small jiffy program called add_element to do this - a .tar.gz file with the source code and a README file (explaining how to compile and run the jiffy) can be downloaded from the prerelease area.


4. REFMAC5
Date: 22/03/2001

Under some strict compilers (e.g. Portland Group), REFMAC5 may fail trying to open the same file on two different unit numbers simultaneously.

Apply the following patch to $CPROG/refmac5_/lsq_newdic_rest.f and remake refmac5:

diff -c -r1.4 lsq_newdic_rest.f
*** lsq_newdic_rest.f   2001/02/28 18:12:55     1.4
--- lsq_newdic_rest.f   2001/03/22 09:35:55
***************
*** 3644,3649 ****
--- 3644,3651 ----
        ENDIF   
        GOTO 10
   999  CONTINUE
+       CLOSE(ISCRB)
+       ISCRB = 0
        RETURN
        END
  C

(Thanks to Ian Tickle)


5. MAPLIB
Date: 01/06/2001

NB: a "broken" version of this fix was originally posted here on 20/03/2001 - under certain systems it generated corrupted values for the mean and rms densities in the map header.

If you have already applied the earlier version of the patch then the second patch needed to fix the problem is:

diff -c -r1.36.2.1 -r1.36.2.2
*** maplib.f    2001/03/22 17:17:23     1.36.2.1
--- maplib.f    2001/06/01 08:55:47     1.36.2.2
***************
*** 374,380 ****
          ARMS  = 0.0
          SUMRHO = 0.0
          SUMRH2 = 0.0
!         OFFSTR = 2.0*QOFFSET
          DO 30 I = 1,20
            DO 20 J = 1,10
              READ (BLANK,FMT=6002) LABELS(I,J)
--- 374,380 ----
          ARMS  = 0.0
          SUMRHO = 0.0
          SUMRH2 = 0.0
!         OFFSTR = 2.0*QOFFST
          DO 30 I = 1,20
            DO 20 J = 1,10
              READ (BLANK,FMT=6002) LABELS(I,J)

Otherwise, the full corrected patch is below.

Many apologies for any inconvenience this has caused, and to Ian Tickle (who's original fix was mangled) - pjb

If a program creates several maps in the same run then the second (and subsequent) maps may have random values for the mean and RMS densities - this is because the sums are not being re-initialised in maplib.

Apply the following patch to $CLIBS/maplib.f to fix this:

diff -c -r1.36 -r1.36.2.2
*** maplib.f    2000/02/25 13:24:47     1.36
--- maplib.f    2001/06/01 08:55:47     1.36.2.2
***************
*** 330,342 ****
        COMMON /MOHDR/NC,NR,NS,MODE,NC1,NR1,NS1,NXYZ(3),CEL(6),MAPCRS(3),
       +       AMIN,AMAX,AMEAN,ISPG,NSYMBT,LSKFLG,SKWMAT(3,3),SKWTRN(3),
       +       JUNK(17),ARMS,NLAB,LABELS(20,10),NCHITM,ITMHDR,ITMSC1
        COMMON /MSTRM/LSTRM(12)
  C     ..
  C     .. Equivalences ..
        EQUIVALENCE (NC,HEADER(1))
  C     ..
  C     .. Save statement ..
!       SAVE /MSTRM/,/MOHDR/,FILE
  C     ..
  C     .. Data statements ..
  C
--- 330,345 ----
        COMMON /MOHDR/NC,NR,NS,MODE,NC1,NR1,NS1,NXYZ(3),CEL(6),MAPCRS(3),
       +       AMIN,AMAX,AMEAN,ISPG,NSYMBT,LSKFLG,SKWMAT(3,3),SKWTRN(3),
       +       JUNK(17),ARMS,NLAB,LABELS(20,10),NCHITM,ITMHDR,ITMSC1
+ 
+       COMMON /MOHSUM/  SUMRHO, SUMRH2, OFFSTR
+       DOUBLE PRECISION SUMRHO, SUMRH2, OFFSTR
        COMMON /MSTRM/LSTRM(12)
  C     ..
  C     .. Equivalences ..
        EQUIVALENCE (NC,HEADER(1))
  C     ..
  C     .. Save statement ..
!       SAVE /MSTRM/,/MOHDR/,/MOHSUM/,FILE
  C     ..
  C     .. Data statements ..
  C
***************
*** 369,374 ****
--- 372,380 ----
          AMAX = -99999999.0
          AMEAN = 0.0
          ARMS  = 0.0
+         SUMRHO = 0.0
+         SUMRH2 = 0.0
+         OFFSTR = 2.0*QOFFST
          DO 30 I = 1,20
            DO 20 J = 1,10
              READ (BLANK,FMT=6002) LABELS(I,J)

(Thanks to Ian Tickle)


6. rotgen.f
Date: 29/03/2001

Attempts to run the Strategy in Rotgen fail with:

Error message: Error opening symmetry operators file (SYMOP) 

The environmental variable SYMOP is not set. Set the environment variable SYMOP to point to $CLIBD/symop.lib

A related problem; a call to CCPFYP is missing from rotgen.f. This will allow the setting of SYMOP from the command line:

diff -c -r1.1 -r1.2
*** rotgen.f    2000/10/24 13:37:16     1.1
--- rotgen.f    2001/03/29 08:59:07     1.2
***************
*** 240,245 ****
--- 240,246 ----
  C
        CALL INIT_FLAGS
        CALL INIT_SETTINGS
+       CALL CCPFYP
        CALL MTZINI
  C
  C====== Initialise the xdl_view routines
(Thanks to Dave Love)
7. rwbrook.f
Date: 25/04/2001

An error in the rwbrook library disables the fractional conversion for pdb files when REMARK 290 SYMTRY is present. This has the knock-on effect that calls to XYZCOORD to return FRACTIONAL coordinates are disabled. As yet this is only known to affect acorn. The following corrects this:

diff -c -r1.62 -r1.61
*** rwbrook.f   2001/04/25 07:53:10     1.62
--- rwbrook.f   2001/04/23 10:45:28     1.61
***************
*** 304,310 ****
        PARAMETER (MAXFILESOPEN=90,MAXSYM=96)
  C     ..
  C     .. Arguments ..
!       INTEGER IFAIL,IUNIT,ICRYST,II,III,JJ,K,ISYM
        REAL AM,BM,RCHK1,RCHK2,FAC
        CHARACTER*(*) FILTYP,LOGNAM,RWSTAT
  C     ..
--- 304,310 ----
        PARAMETER (MAXFILESOPEN=90,MAXSYM=96)
  C     ..
  C     .. Arguments ..
!       INTEGER IFAIL,IUNIT,ICRYST,II,JJ,K,ISYM
        REAL AM,BM,RCHK1,RCHK2,FAC
        CHARACTER*(*) FILTYP,LOGNAM,RWSTAT
  C     ..
***************
*** 460,466 ****
               READ(BROOKA(11:18),'(I8)')NSYMCHK
               CALL  symfr2 (BROOKA,22,nsymchk,rsymchk)
                write(6,'(a,i3,4(/,4f10.3))')' remark 290',nsymchk,
!      + ((rsymchk(iii,jj,nsymchk),iii=1,4),jj=1,4)
             ENDIF
            ENDIF
  C
--- 460,466 ----
               READ(BROOKA(11:18),'(I8)')NSYMCHK
               CALL  symfr2 (BROOKA,22,nsymchk,rsymchk)
                write(6,'(a,i3,4(/,4f10.3))')' remark 290',nsymchk,
!      + ((rsymchk(ii,jj,nsymchk),ii=1,4),jj=1,4)
             ENDIF
            ENDIF
  C
(Thanks to Eleanor Dodson)
8. detwin.f
Date: 26/04/2001

A minor bug in detwin produces confusing output in the summary, where the twinning fraction used for the output mtz file is alway reported as 0.48. This does not affect the running of the program. This also occurs for CCP4 version 4.0.x

diff -c -r1.7.2.1 -r1.7
*** detwin.f    2001/04/25 15:23:37     1.7.2.1
--- detwin.f    2000/06/15 09:23:45     1.7
***************
*** 863,869 ****
        if(twfac.gt.0.001)call lwclos(mtzout, iprint)
  c
        call ccp4h_summary_beg()
!       write(6,1020) twfac,nout,nequ,nmiss
   1020 format(/,
       +    'Output file written for  twinning fraction',f6.3,/, 
       +    'Number of reflections written to output file',I7,/,
--- 863,869 ----
        if(twfac.gt.0.001)call lwclos(mtzout, iprint)
  c
        call ccp4h_summary_beg()
!       write(6,1020) alpha,nout,nequ,nmiss
   1020 format(/,
       +    'Output file written for  twinning fraction',f6.3,/, 
       +    'Number of reflections written to output file',I7,/,
(Thanks to Dr Nicholas Keep for spotting this)
9. areaimol
Date: 11/05/2001

AREAIMOL cannot treat ANISOU cards correctly in input PDB files - you will get additional phantom atoms which will distort the accessible surface area values and the analyses.

Please download and install a fixed versions of AREAIMOL from the areaimol-110501.f file on the prerelease area.

(Thanks to John Jenkins for reporting this)


10. combat
Date: 15/06/2001

There is a problem with the INPUT USER option of COMBAT - it doesn't work.

A fixed version of the combat files can be downloaded as the file combat-080801.tar.gz from the prerelease area.

Note that this updated version has some other changes to the version distributed with 4.1.1 - most noticeably: the MTZF option now accepts F(+) and F(-) as an alternative to mean F, and the MISBATCH option has been removed: the program now only outputs batches which are present in the input file.
It also fixes a more recently discovered bug, see below.


11. rfcorr.f Date: 29/03/2001

Ian Tickle reports that changes made between version 4.0 and 4.1* have broken the program. There is also another minor fix where an array is uninitialsed and causes problems on some OSs.

A fix is available on the prerelease area.


12. act
Date: 16/07/2001

act fails to recognise HOH as solvent, confusing it with HIS, when it has non-zero occupancy. This is corrected by moving the test for solvent before that for the main chain atoms in BSTATS.

A fix is available on the prerelease area.


13. combat
Date: 08/08/2001

COMBAT sets the lattice type wrongly for centred spacegroups in MTZ files - it is always set to "P".

A fixed version (which also includes the fixes for earlier reported problems) can be downloaded as the file combat-080801.tar.gz from the prerelease area.

(Thanks to Phil Evans for fixing this)


14. LIBCHECK
Date: 11/09/2001

On some systems LIBCHECK may crash when trying to load certain library descriptions e.g. MO6. This problem occurs whether the program is run from the command line or from the Monomer Library Sketcher interface in CCP4i.

The following patch must be applied to $CPROG/refmac5_/libcheck.f:

*** libcheck.f  2001/01/22 14:37:44     1.6
--- libcheck.f  2001/09/11 13:34:39     1.7
***************
*** 3141,3147 ****
        CALL NB_VMOD(V2,AV2)
        CALL NB_VPROD(V1,V2,S)
        COSA1= S/(AV1*AV2)
!       ANG1 = ACOS(COSA1)
        ANG1 = PI-ANG1
  C --
  C ----Tabl. I4 AV THETA --------------------------------
--- 3141,3147 ----
        CALL NB_VMOD(V2,AV2)
        CALL NB_VPROD(V1,V2,S)
        COSA1= S/(AV1*AV2)
!       ANG1 = ACOS(AMAX1(AMIN1(COSA1,1.0),-1.0))
        ANG1 = PI-ANG1
  C --
  C ----Tabl. I4 AV THETA --------------------------------
***************
*** 5555,5561 ****
        CALL NB_VMOD(V2,AV2)
        CALL NB_VPROD(V1,V2,S)
        COSA1= S/(AV1*AV2)
!       ANG1 = ACOS(COSA1)
        ANG1 = PI-ANG1
  C --
  C ----Tabl. I4  --------------------------------
--- 5555,5561 ----
        CALL NB_VMOD(V2,AV2)
        CALL NB_VPROD(V1,V2,S)
        COSA1= S/(AV1*AV2)
!       ANG1 = ACOS(AMAX1(AMIN1(COSA1,1.0),-1.0))
        ANG1 = PI-ANG1
  C --
  C ----Tabl. I4  --------------------------------
(Thanks to Garib Murshudov)
15. COORDCONV
Date : 12/09/2001

There are two problems with coordconv:

  1. The program does not behave as described in the documentation, it requires that any non-standard orthogonalisation code (anything other than 1, essentially) must be explicitly specified via the ORTH subkeyword in order to transform coordinates correctly.
  2. The program cannot reorthogonalise PDB files in a single step; it is necessary to perform reorthogonalisation in two steps, for example by going via FRAC coordinates:
    coordconv xyzin orig.pdb xyzout tmp.frac <<eof-1
    INPUT PDB ORTH 5 
    OUTPUT FRAC
    CELL 9.488 16.853 31.684 95.77 98.07 99.4500
    eof-1
    
    coordconv xyzin tmp.frac xyzout reorth.pdb <<eof-2
    INPUT FRAC
    OUTPUT PDB ORTH 1
    CELL 9.488 16.853 31.684 95.77 98.07 99.4500
    eof-2
    
    Note that PDBSET has a REORTHOGONALIZE keyword which can also be used to switch between different orthogonalisations.
Unfortunately no fixes are available for these problems at present.

(Thanks to Nick Keep)


16. $CLIBS/symlib.f
Date : 09/10/2001

It has long been known that there are problems with some ccp4 probrams compiled under Linux RedHat 7.0 and 7.1. If your compilers are uptodate (gcc version 2.94-85) or are the RedHat 7.1 native compiler replacing the $CLIBS/symlib.f solves the majority of these problems. However, caution is still recomended. A fixed symlib.f (symlib270921.f) is available on the prerelease area.

(Thanks to Garib Murshudov)

Date : 16/11/2001

The limits of the real-space asymmetric unit for I212121 listed in s/r SETLIM are wrong. A fixed symlib.f (symlib.f) is available on the prerelease area.


17. COMBAT and ROTAPREP
Date : 23/10/2001

Apparently scalepack will sometimes (probably more recent version) subtract the batch number by 1 - giving you a batch number of zero. Zero is not a legitimate batch number in a multibatch mtz file so addbatch must be set to at least 1. This has shown to be a problem when outputting with scalepack option "nomerge original indices" with a very recent version of the HKL package.

This problem can be spotted as combat (and rotaprep) give the obscure message:

 ***  Error
 From LWBSETID : no batches present to write to!
 combat:  *** Program Terminated
 Times: User:       0.8s System:    0.1s Elapsed:    0:01


18. MAPMASK
Date : 25/10/2001

The EXTEND COPY mode is badly broken. A new version of the $CPROG/mapmask_/mapmask.f file can be found as mapmask-251001.f on the prerelease area. Recompiling mapmask with the updated file should fix the problem.

(With thanks to Kevin Cowtan)


19. sftools
Date : 31/01/2002

Clemens Vonrhein vonrhein@globalphasing.com: there is a bug in the EXPAND and REDUCE routine when a phase shift is necessary and the input file contains a mixture of phases (type 'P') and Hendrickson-Lattman coefficients (type 'A'). Re-using the pshft variable for the C and D HLs means that columns of types 'A' or 'P' _following_ the first set of Hls are treated wrong.

diff:

3311c3311
<       real pshft,phares,packmat(9),gt_real,phashft,value,inrange
---
>       real pshft,pshft2,phares,packmat(9),gt_real,phashft,value,inrange
3423,3425c3423,3425
<               pshft=pshft*2
<               ref(kpos+2)=value*cos(pshft)-ref(kpos+3)*sin(pshft)
<               ref(kpos+3)=value*sin(pshft)+ref(kpos+3)*cos(pshft)
---
>               pshft2=pshft*2
>               ref(kpos+2)=value*cos(pshft2)-ref(kpos+3)*sin(pshft2)
>               ref(kpos+3)=value*sin(pshft2)+ref(kpos+3)*cos(pshft2)
9245c9245
<       real pshft,phares,value,inrange
---
>       real pshft,pshft2,phares,value,inrange
9353,9355c9353,9357
<                 pshft=pshft*2
<                 ref(noff+k+2)=value*cos(pshft)-ref(noff+k+3)*sin(pshft)
<                 ref(noff+k+3)=value*sin(pshft)+ref(noff+k+3)*cos(pshft)
---
>                 pshft2=pshft*2
>                 ref(noff+k+2)=value*cos(pshft2)-
>      .               ref(noff+k+3)*sin(pshft2)
>                 ref(noff+k+3)=value*sin(pshft2)+
>      .               ref(noff+k+3)*cos(pshft2)

Line numbers may vary slightly.

CCP4i


1. prephadata.script
Date : 9/3/2001.

In the 'Prepare Data for HA Search' task the input 'SAD data as F+F-' to prepare data for Rantan does not output the correct MTX column labels to the command file.

Download a fixed prephadata.script from the prerelease area.


2. loggraph.tcl
Date : 15/3/2001

An error in $CCP4I_TOP/bin/loggraph.tcl means that if loggraph is run before ccp4i the configure.def file will not be created correctly. The stack trace:

  Running auto-configure for configure
  Creating new configure parameters file
  /prog/ccp4/4.1.1/ccp4i/etc/unix/configure.def
  Error in startup script: invalid command name "SaveArray"
      while executing
  "SaveArray $taskname $filename $arrayname -save_types"
      (procedure "InitialisePreferences" line 45)
      invoked from within
  "InitialisePreferences configure configure"
      (file "/prog/ccp4/4.1.1/ccp4i/bin/loggraph.tcl" line 52)
      invoked from within
  "source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
      (file "/prog/ccp4/4.1.1/ccp4i/bin/loggraph" line 5)

The following patch corrects this:


diff -C1 -c -r1.1 -r1.1.2.1
*** loggraph.tcl        2000/11/14 17:50:44     1.1
--- loggraph.tcl        2001/03/16 08:48:10     1.1.2.1
***************
*** 43,44 ****
--- 43,45 ----
  source [file join $env(CCP4I_TOP) src system.tcl]
+ source [file join $env(CCP4I_TOP) src utils.tcl]

Alternatively, ccp4i should be run first.


3. Install New Task
Date : 4/4/2001.

The Install New Task option has some problems:

Download a fixed version of $CCP4I_TOP/src/database.tcl from the prerelease area.

Please note that this an update on the last fix to database.tcl, which was dated 27/3/2001.


4. Accidental deletion of directories prior to running a job
Date : 3/4/2001.

This is an extremely undesirable feature of the interface which may manifest itself under certain special circumstances - if a user accidentally assigns the output file name for a task to be an existing directory (for example, by clicking on OK in the file browser without selecting a file), and then tries to run the task, then CCP4i will give them the option of deleting the existing ``file''. Clicking on OK at this point will result in the deletion of both the directory and its contents.

Note that the directory is only deleted if the user selects OK - if ``Abort'' is chosen instead then nothing happens.

A patched version of the file $CCP4I_TOP/src/runjob.tcl can be obtained from the prerelease area. Using this version CCP4i should warn when the output ``file'' is actually a directory, and will not give the option to delete it but simply abort the run.

(Thanks to Nick Keep and David Knight for reporting this.)


5. loggraph
Date : 5/4/2001.

loggraph cannot open a file selected from the ``Open File'' option in the file menu, and the default directory alias is always blank.

Download a fixed $CCP4I_TOP/loggraph/loggraph.tcl from the prerelease area.


6. amore
Date : 2/5/2001

translation function with known solutions will misorder the models. The following corrects this fault in $CCP4I_TOP/utils/amore_utils.tcl:

diff -c -r1.5 amore_utils.tcl
*** amore_utils.tcl     2001/03/13 16:20:05     1.5
--- amore_utils.tcl     2001/04/30 08:31:12
***************
*** 353,359 ****
      set sol ""
      foreach im $imodel_list {
        incr nl
!       append sol "SOLUTION $fix $im [lrange [lindex $input_list $nl] 2 end]\n"
      }
      if { $solution0 != "" } { 
        foreach s0 $solution0 {
--- 353,360 ----
      set sol ""
      foreach im $imodel_list {
        incr nl
!       set mc [ lindex [lindex $input_list $nl] 1 ]
!       append sol "SOLUTION $fix [lindex $imodel_list [expr $mc -1] ] [lrange [lindex $input_list $nl] 2 end]\n"
      }
      if { $solution0 != "" } { 
        foreach s0 $solution0 {

7. solomon
Date : 29/8/2001

typo in $CCP4I_TOP/scripts/solomon.script effects the sigmaa component.

diff -r1.3 -r1.2 solomon.script
140c140
<   set FP $FO
---
>   set FP $F0
(thanks to Yen-Chywan Liaw)
8. contact
Date : 29/8/2001

Several problems with the contact interface. The interchain option without ranges, and the intermolecular option both fail. The contact.tcl and contact.com in the prerelease area fix these.
(thanks to Dr. Nick Keep)


9. Monomer Library Sketcher
Date : 12/09/2001

  1. Sketcher may fail on some systems when attempting to load certain monomers from the library. The problem is not with the Sketcher itself, but with the underlying libcheck program - see the relevant section above for details of how to fix this problem.
  2. The Load from Library option under Read only lists the first three letters of the monomer code names. Most codes are only three characters but for some sugars, in particular, they are longer. This will be fixed in the next release.

10. ARP/wARP
Date : 17/09/2001

When running refinement with ARP/wARP under CCP4i, the job may fail with a message from ARP such as:

The program run with command: arp_warp XYZIN
/disk3/cirilli/PROJECTS/ABAD/CCP4/6nov.pdb MAPIN1
/tmp/abad_test_1_5_mapin_1.tmp MAPIN2 /tmp/abad_test_1_6_mapin_2.tmp XYZOUT
/disk3/cirilli/PROJECTS/ABAD/CCP4/6nov_arp1.pdb 
has failed with error message child process exited abnormally

You need to check which version of ARP/wARP you are running - the latest version (5.1) from the EMBL is not compatible with CCP4i, which requires an older version (5) which is distributed with CCP4 4.1.*.

If the interface is using the `wrong' version of ARP then it has to be configured to pick up the correct version as follows:

  1. Find the full path for the CCP4-distributed arp_warp program (it will probably be the same as $CBIN/arp_warp).
  2. Start up the interface and go to the System Administration option on the right-hand menu of the main window.
  3. Select Configure Interface and look for the section called External Programs in the window which appears.
  4. At the bottom there is a line saying Give full path name for CCP4 programs to overcome name conflicts - click on Add Program, enter arp_warp in the left hand box and the full path (including the program name) in the right hand one.
  5. Save the configuration and restart the interface.

11. lsqkab graphs
Date : 2/10/2001

When running lsqkab through ccp4i (superpose) the requested rms table will not display under loggraph. This is due to a double processing of the output table, which results in two headers. A quick fix is to remove the second header. A version of superpose.script which fixes this problem is on the prerelease area.


12. fffear
Date : 17/10/2001

Some of the names in the menu of library fragments (in fact, the last three in the menu: "theoretical-10-helix", "theoretical-5-strand" and "theoretical-10-strand") are mixed up, and if selected will use a different fragment when the program actually runs.

The fix is to download a new version of the fffear.tcl file from the prerelease area to replace the existing version in $CCP4/ccp4i/tasks/.


13. XtalView maps from Refmac5
Date : 19/02/2002

Errors in two files cause the child script to crash. This manifests itself in the refmac job keeping the running status even after finishing. The map output file will also have spurious lines in it.

The fix is to download new versions of refmac_maps.script (replaces existing version in $CCP4/ccp4i/scripts) and map_utils.tcl (replaces version in $CCP4/ccp4i/utils). Both are available from the prerelease area. Or, to apply the following:

*** refmac_maps.script  2000/11/14 18:25:48     1.2
--- refmac_maps.script  2002/02/19 13:52:03     1.4
***************
*** 38,42 ****
          foreach line $hkl_in {
            append hkl_out [format "%5i%5i%5i%12.1f%12.1f%12.1f" \
                [lindex $line 0 ] [lindex $line 1 ] [lindex $line 2 ] \
!               [lindex $line 3 ] 1.0 [lindex $line 4]] \n
          }
--- 38,43 ----
          foreach line $hkl_in {
+           catch {
            append hkl_out [format "%5i%5i%5i%12.1f%12.1f%12.1f" \
                [lindex $line 0 ] [lindex $line 1 ] [lindex $line 2 ] \
!               [lindex $line 3 ] 1.0 [lindex $line 4]] \n }
          }

*** map_utils.tcl       2001/03/13 16:20:06     1.6
--- map_utils.tcl       2002/02/19 13:34:15     1.7
***************
*** 165,167 ****
      set n -1; foreach lab $xtal_labin { incr n
!       append text " [subst $lab]=[lindex $labin $n]"
      }
--- 165,168 ----
      set n -1; foreach lab $xtal_labin { incr n
!       if { $n < [llength $labin] } {
!         append text " [subst $lab]=[lindex $labin $n]" }
      }

Tutorials and Examples


1. CCP4 Tutorial: Session 2 / Data Processing
Date : 30/04/2001.

at stage 2.3 we're told to de-select the radio button:
keep the input intensities in the output MTZ file
but I found that I also needed to de-select the button:
Ensure unique data & add FreeR column for 0.05 fraction of data.
(if ive understood it correctly if you do choose to select this then you can skip step 2b! But I never said that!)

The html fix will be in the next release. Alun Ashton 30/04/2001



Problems with 4.1


Installation


1. XDL_VIEW Libraries: on some systems with the GNU autoconf tools there may be a problem with the xdl_view library installation failing, due to corruption of the xdl_view configure and Makefiles when running the main configure script.

The problem can be avoided by updating the timestamps on a number of files before running configure, as follows:

> cd $CCP4/x-windows/xdl_view/src
> touch configure.in && sleep 1
> touch Makefile.am && sleep 1
> touch aclocal.m4 && sleep 1
> touch configure && sleep 1
> touch Makefile.in && sleep 1
Unfortunately if the installation fails and the files are corrupted then the only way to restore the correct versions is to download and unpack the x-windows files again first - for example the pub/ccp4/ccp4/ccp4-4.1/x-windows.tar.gz file on the ccp4 ftp server - and then applying the above work-around.

(Thanks to Clemens Vonrhein.)


2. x-windows: the 'make distclean' target in the $CCP4/x-windows Makefile.in is incomplete - it doesn't do a full cleanup in some of the subdirectories (e.g. rotgen) and leaves behind config.status files. Also the empty-targets option was broken.

Apply the following patch to $CCP4/x-windows/Makefile.in to obtain the correct behaviour:

diff -c -r1.23 -r1.26
*** Makefile.in 2000/12/14 14:04:07     1.23
--- Makefile.in 2001/02/02 09:48:42     1.26
***************
*** 160,166 ****
  #
  # install - not yet installed!
  #
! install_obj = ipdisp/ipdisp ipdisp.exe hklview xdldataman xdlmapman \
  rotgen mosflm
  install: all
        $(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir)
--- 160,166 ----
  #
  # install - not yet installed!
  #
! install_obj = ipdisp.exe hklview xdldataman xdlmapman \
  rotgen mosflm
  install: all
        $(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir)
***************
*** 187,205 ****
        cd $(libjwc_f_dir) ; $(MAKE) clean ;\
        cd $(mosflm_dir) ; $(MAKE) realclean
  distclean: realclean
!       -rm -rf Makefile config.statusempty-targets:
!       for i in $(install_obj) ; do \
!         test -s $$i && rm -f $$i && touch $$i || true ;\
!       done
  uninstall: 
        for i in $(install_obj); do \
          rm -f $(bindir)/$$i ;\
        done
        cd $(xdlview_dir) ; $(MAKE) uninstall ;\
        cd $(libjwc_c_dir) ; $(MAKE) uninstall ;\
        cd $(libjwc_f_dir) ; $(MAKE) uninstall
        test -f $(libdir)/font.bin && rm -f $(libdir)/font.bin ; \
        test -f $(libdir)/nice_font.bin && rm -f $(libdir)/nice_font.bin
  
  FORCE : ;
  
--- 187,217 ----
        cd $(libjwc_f_dir) ; $(MAKE) clean ;\
        cd $(mosflm_dir) ; $(MAKE) realclean
  distclean: realclean
!       -rm -rf Makefile config.status ;\
!       cd $(xdlview_dir) ; $(MAKE) distclean ;\
!       cd $(rotgen_dir) ; $(MAKE) distclean ;\
!       cd $(libjwc_c_dir) ; $(MAKE) distclean ;\
!       cd $(libjwc_f_dir) ; $(MAKE) distclean
  uninstall: 
        for i in $(install_obj); do \
          rm -f $(bindir)/$$i ;\
        done
+       rm -f $(bindir)/ipdisp ;\
        cd $(xdlview_dir) ; $(MAKE) uninstall ;\
        cd $(libjwc_c_dir) ; $(MAKE) uninstall ;\
        cd $(libjwc_f_dir) ; $(MAKE) uninstall
        test -f $(libdir)/font.bin && rm -f $(libdir)/font.bin ; \
        test -f $(libdir)/nice_font.bin && rm -f $(libdir)/nice_font.bin
+ 
+ # this leaves empty, non executable files in place of the targets which have
+ # been built, saving space in the build directory, but enabling re-building
+ # contingent on the empty files being out-of-date with respect to their
+ # dependencies. 
+ 
+ empty-targets :
+       -for i in $(install_obj); do \
+         test -s $$i && rm -f $$i && touch $$i || true ;\
+       done
  
  FORCE : ;

(Thanks to Clemens Vonrhein, Katherine McAuley and Nobuhisa Watanabe.)


3. mosflm/filec: an error in the configure script means that FORTRAN compiler options are included in the filec compilation instead of C compiler options. This effects the irix64, linux_compaq_compilers, and linux system options. Compilation with fail for the irix64.

Apply the following patch to $CCP4/configure to obtain the correct behaviour.

cvs diff -r1.125 configure
< # $Id: configure,v 1.125 2001/01/26 15:30:46 pjx Exp $
---
> # $Id: configure,v 1.126 2001/01/31 14:41:52 pjx Exp $
771c771
<                filec_CFLAGS='$XFFLAGS $FOPTIM -Dsgi' \
---
>                filec_CFLAGS='$XCFLAGS $FOPTIM -Dsgi' \
1279c1279
<                filec_CFLAGS='$XFFLAGS $FOPTIM -Dlinux' "}
---
>                filec_CFLAGS='$XCFLAGS $FOPTIM -Dlinux' "}
1312c1312
<                filec_CFLAGS='$XFFLAGS $FOPTIM -Dlinux' \
---
>                filec_CFLAGS='$XCFLAGS $FOPTIM -Dlinux' \

(Thanks to Pete Dunten)


4. Portland Group Compilers: There are a couple of reported problems using Portland Group FORTRAN compiler pgf77 under Linux:
  1. lib/src/library.c must NOT be compiled with -DG77 because this triggers an "inconsistent declaration of f_exit()".
    Run configure linux options, edit the resulting config.status file, and then rerun before building.
  2. REFMAC5 will not compile unless the two patches below (in the "Programs" section) are applied to the appropriate files.

(Thanks to Ethan Merritt)


5. mapslicer/ccp4mapwish: Compilation may fail for certain versions of the Tcl/Tk libraries, e.g. 8.3, with the complaint that Tk_Main is an unresolved symbol.

The fix to $CPROG/ccp4mapwish_/c_scr/ccp4mapwish.c is:

diff -c -r1.2 ccp4mapwish.c
*** ccp4mapwish.c       2001/02/19 08:01:24     1.2
--- ccp4mapwish.c       2001/02/20 08:47:53
***************
*** 30,35 ****
--- 30,37 ----
     Must be version 8.0 or better */
  #include <tcl.h>
  
+ #include <tk.h>
+ 
  /* Application-specific definitions and prototypes */
  #include    /* CCP4 machine dep. include file */
  #include "ccp4mapwish.h"
Note that further fixes need to be applied for run-time bugs (see below).
6. LAPACK: There is a potential problem with the ordering of the BLAS and LAPACK libraries specified by configure and written to Makefile headers at installation time.

If both BLAS and LAPACK libraries are needed then the BLAS library must be specified after LAPACK, since the loader only reads symbols once. To fix this, make the following change to $CCP4/configure:

***************
*** 1812,1818 ****
      cd ../..
      #
      lapackdir=lib/lapack
!     XLAPACK_LIB="-L$BLASDIR -l$BLASLIB -L$srcdir/lib/lapack -llapack"
    fi
    # Clean up
    if test -f testlink.f || test -f testlink ; then
--- 1812,1818 ----
      cd ../..
      #
      lapackdir=lib/lapack
!     XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB"
    fi
    # Clean up
    if test -f testlink.f || test -f testlink ; then

Programs


1. sfcheck a missing arguement in a function call can cause sfcheck to crash. The call is in the postscript writing routines, and, therefore, should not effect the other results of the program where no crash has occured.

Apply the following patch to correct the call

diff -c sfch_graph_2.f sfch_graph_2.f_old
*** sfch_graph_2.f      Mon Feb  5 17:18:17 2001
--- sfch_graph_2.f_old       Mon Jan 29 15:20:12 2001
***************
*** 396,402 ****
                 CALL LSCALE (XR,YH6,-BMH,-TLEN,3,0.0,MAXDENSID,.FALSE.)
                 CALL LSCALE (XR,YL7,BMH,-TLEN,2,0.0,MAXBFACT,.FALSE.)
                 CALL LSCALE (XR,YH8,-BMH,-TLEN,2,0.0,MAXBFACT,.FALSE.)
!                CALL LSCALE (XR,YL9,BMH,-TLEN,2,0.0,1.0,.FALSE.)
                 IF ((XCHSTRT .GT. 0).AND.(XCHSTRT.NE.XR)) THEN
                    CALL CHAINBOX (XCHSTRT,XR,YL,CHAINID)
                 ENDIF
--- 396,402 ----
                 CALL LSCALE (XR,YH6,-BMH,-TLEN,3,0.0,MAXDENSID,.FALSE.)
                 CALL LSCALE (XR,YL7,BMH,-TLEN,2,0.0,MAXBFACT,.FALSE.)
                 CALL LSCALE (XR,YH8,-BMH,-TLEN,2,0.0,MAXBFACT,.FALSE.)
!                CALL LSCALE (XR,YL9,BMH,-TLEN,2,1.0,.FALSE.)
                 IF ((XCHSTRT .GT. 0).AND.(XCHSTRT.NE.XR)) THEN
                    CALL CHAINBOX (XCHSTRT,XR,YL,CHAINID)
                 ENDIF

2. molrep: there are currently two reported problems.
  1. On some systems (only IRIX so far) MOLREP may fail soon after startup with a message of the form:
    inwrite: off end of record
    *** Execution terminated (110)
    

    The problem is in the file $CPROG/molrep_/main_molrep_mtz.f - apply the following patch to fix:

    diff -r1.5 main_molrep_mtz.f
    215c215
    <       WRITE(LINE,*) '--- MTZ file : ',FILE_MTZ(1:L)
    ---
    >       WRITE(LINE,'(A,A)') '--- MTZ file : ',FILE_MTZ(1:L)
    
  2. molrep may crash due to undefined files. The exhibites itself for MODE S for non-P1 symmetry.

    Apply the following patches

    diff -c molrep_prog.f ccp4-4.1/src/molrep_/molrep_prog.f
    *** molrep_prog.f       Mon Feb 19 11:11:16 2001
    --- ccp4-4.1/src/molrep_/molrep_prog.f Mon Jan 29 15:18:39 2001
    ***************
    *** 3283,3289 ****
      C ----------------------------------------   
            NAME=NAMED
            IF(NSYM.GT.1) THEN
    -         MTF = 43
              NAME='molrp_scratch_rdc'
              PATH=' '
              EXT='dat'
    --- 3283,3288 ----
    
    diff -c molrep.f ccp4-4.1/src/molrep_/molrep.f
    *** molrep.f    Mon Feb 19 11:18:45 2001
    --- ccp4-4.1/src/molrep_/molrep.f      Wed Feb  7 16:54:52 2001
    ***************
    *** 5295,5301 ****
      C ---
            NP = RESULTA(1,12) 
            IF(NP.LE.0.0) GO TO 900       
    !       IOUT = 11
            NAME = 'molrep_srf.tab'
            PATH = ' '
            EXT  = ' '
    --- 5295,5301 ----
      C ---
            NP = RESULTA(1,12) 
            IF(NP.LE.0.0) GO TO 900       
    ! 
            NAME = 'molrep_srf.tab'
            PATH = ' '
            EXT  = ' '
    
    (Thanks to Arthur J. Chirino)

3. areaimol: in some cases the +/-1 lattice vector search will not be sufficient to find all crystallographically-related molecules which contact the original molecule (see keyword TRANS) and so areas will wrongly appear to be exposed.

A version of AREAIMOL which automatically searches +/-2 lattice vectors is available on the prerelease area, as areaimol-080201.f This updated version should work in these situations, and find all the buried area correctly.

(Thanks to David Buckler)


4. oasis: there is a minor bug which can cause the program to crash with a memory-related error shortly after start-up. The fix is to change the following line:
diff -r1.6 oasis.f
508c508
<       IFLAG(I) = 1
---
>       IFLAG(J) = 1

5. refmac5: there are two minor bugs in REFMAC5 which will give an error when compiling using the Portand Group FORTRAN compiler pgf77 under Linux (see also "Installation" above) unless corrected with the following patches:
  1. $CPROG/refmac5_/solvent_contr_mask.f:
    Extra comma should be removed:
    diff -c -r1.3 solvent_contr_mask.f
    *** solvent_contr_mask.f        2001/01/22 14:32:42     1.3
    --- solvent_contr_mask.f        2001/02/15 17:11:20
    ***************
    *** 412,418 ****
            NSEC    = N3
            IUN_MAP = 0
            TITLE   = 'Mask from refmac'
    !       CALL MWRHDL(IUN_MAP,'MSKOUT',,TITLE,NSEC,IUVW,MXYZ,
           &      NW1,NU1,NU2,NV1,NV2,CELL_LOCAL,LSPGRP,LMODE)
      C
            MU = N1
    --- 412,418 ----
            NSEC    = N3
            IUN_MAP = 0
            TITLE   = 'Mask from refmac'
    !       CALL MWRHDL(IUN_MAP,'MSKOUT',TITLE,NSEC,IUVW,MXYZ,
           &      NW1,NU1,NU2,NV1,NV2,CELL_LOCAL,LSPGRP,LMODE)
      C
            MU = N1
    
  2. $CPROG/refmac5_/tls_newdic.f:
    Must declare variable OLINE:
    diff -c -r1.2 tls_newdic.f
    *** tls_newdic.f        2001/01/22 14:38:22     1.2
    --- tls_newdic.f        2001/02/15 17:13:47
    ***************
    *** 371,376 ****
    --- 371,377 ----
      
            INTEGER NPARS
            PARAMETER (NPARS = 200)
    +       CHARACTER OLINE*60
      
      c---Things for parser
            CHARACTER LINE*600,KEY*4,CVALUE(NPARS)*4
    
(Thanks to Ethan Merritt)
6. mapslicer: there are problems when trying to read in maps with sections starting at non-zero section numbers.

This requires a fix to $CPROG/ccp4mapwish_/c_src/ccp4mapwish.c:

diff -r1.1 -r1.2
141c141
<   int   i,j,k, lenname, ifail=0, iunit, nsize;
---
>   int   i,j,k, isec, lenname, ifail=0, iunit, nsize;
270a271
>   /* Section numbering may not start at zero... */
272a274
>       /* Set ifail = 1 to switch on debug mode */
274c276,280
<       getsection_(&iunit, &i, plane = data, &nsize, &ifail);
---
>       /* Section numbering in the map file can start from
>        an arbitrary value
>        Start section is stored in nw1 */
>       isec = i + nw1;
>       getsection_(&iunit, &isec, plane = data, &nsize, &ifail);
691c697
<   section->ulimits[1] = start + map->ext[iu] - 1;
---
>   section->ulimits[1] = map->start[iu] + map->ext[iu] - 1;
693c699
<   section->vlimits[1] = start + map->ext[iv] - 1;
---
>   section->vlimits[1] = map->start[iv] + map->ext[iv] - 1;
696c702,706
<      Once again must think about different possible permutations */
---
>      this_sec points to the "absolute" section number from the mapfile
>      This must be reset relative to the section numbers stored in memory */
>   this_sec = this_sec - start;
> 
>   /* Once again must think about different possible permutations */
1782c1792,1793
<       if ((xlim1 > 1 && xlim2 > 1) && (ylim1 > 1) && (ylim2 > 1))
---
>       if ((fabs(xlim1) > 1.0 && fabs(xlim2) > 1.0)
>         && (fabs(ylim1) > 1.0) && (fabs(ylim2) > 1.0))

7.distang: distang does not recognise WAT as a water residue.

The following is a simple fix.

diff -c distang.f ccp4-4.1/src/distang.f
*** distang.f   Mon Feb 19 16:23:20 2001
--- ccp4-4.1/src/distang.f        Mon Jan 29 15:17:07 2001
***************
*** 229,237 ****
  C          **********************
        CALL RES3TO1(RESNAM,RESNM1)
  C          **********************
! C add extra check to recognise water labelled HOH and WAT
!       IF( RESNAM(1:3) .EQ. 'HOH' .OR.
!      +    RESNAM(1:3) .EQ. 'WAT' ) RESNM1 ='O'
  C
        WRITE (NAME(NAT),FMT='(a1,i4,a4,a1)') RESNM1,IRESCD,ATNAM,CHNNAM
  C
--- 229,236 ----
  C          **********************
        CALL RES3TO1(RESNAM,RESNM1)
  C          **********************
! C add extra check to recognise water labelled HOH
!       IF( RESNAM(1:3) .EQ. 'HOH') RESNM1 ='O'
  C
        WRITE (NAME(NAT),FMT='(a1,i4,a4,a1)') RESNM1,IRESCD,ATNAM,CHNNAM
  C

8. revise: the tables output in revise contain a formatting error which will cause problems in loggraph.

The solution is to use formats that reflect the size of the real.

diff -c revise.f ccp4-4.1/src/revise.f
*** revise.f	Thu Feb 22 18:59:46 2001
--- ccp4-4.1/src/revise.f	Thu Feb 22 18:56:54 2001
***************
*** 1436,1448 ****
       +   '  :Ratio at Whole Resolutions of data ',I2,' over ',I2,
       +   ':N:1,12:',/,'  $$ Ratio ')
           DO 1210 NSS = 1, NRMAX
!           IF(RES(NSS).GE.100.0) THEN
!             WRITE(LUNOUT,'(A,F6.2)') '  Resolution_at_range_',RES(NSS)
!            ELSE IF(RES(NSS).GE.10.0) THEN
!             WRITE(LUNOUT,'(A,F5.2)') '  Resolution_at_range_',RES(NSS)
!            ELSE 
!             WRITE(LUNOUT,'(A,F4.2)') '  Resolution_at_range_',RES(NSS)
!            END IF
   1210    CONTINUE
           WRITE(LUNOUT,FMT='(A)') '  Ratio_at_Whole_Resolution  $$'
           WRITE(LUNOUT,1220) (NSS,NSS=1,NRMAX)
--- 1436,1443 ----
       +   '  :Ratio at Whole Resolutions of data ',I2,' over ',I2,
       +   ':N:1,12:',/,'  $$ Ratio ')
           DO 1210 NSS = 1, NRMAX
!           WRITE(LUNOUT,1205) RES(NSS)
!  1205     FORMAT('  Resolution_at_range_',F5.2)
   1210    CONTINUE
           WRITE(LUNOUT,FMT='(A)') '  Ratio_at_Whole_Resolution  $$'
           WRITE(LUNOUT,1220) (NSS,NSS=1,NRMAX)
(Thanks to Eleanor J. Dodson)
9. mlphare: There is a bug if you are using anisotropic B factors; they are not correctly converted after being read in. The fix is a minor change:
diff -c -r1.97 mlphare.f
*** mlphare.f   2001/02/22 11:12:44     1.97
--- mlphare.f   2001/02/23 16:23:09
***************
*** 4679,4685 ****
  C          a = b*c
  C
  C          **************************
!       CALL MATMUL(BANGST,AMAT,BANGST1)
  C          **************************
  C
  C----   bangst(2) = [amat]*[bangst(1(TRANSPOSE)]
--- 4679,4685 ----
  C          a = b*c
  C
  C          **************************
!       CALL MATMUL(BANGST1,AMAT,BANGST)
  C          **************************
  C
  C----   bangst(2) = [amat]*[bangst(1(TRANSPOSE)]

Documentation


1. tutorial2000: the Molecular Replacement tutorial using AMoRe ($CEXAM/tutorial2000/html/mr-tutorial-amore.html) has some typos.
  1. Reference to the file mr_model.pdb in the $CEXAM/tutorial2000/data directory - in fact this should be the file model.pdb which is used in the main Molecular Replacement tutorial.
  2. Reference to the ..mr_fix.mr file should actually be ..mr_fit.mr

There is an additional omission from the $CEXAM/tutorial2000/results directory: the file model_molrep1.pdb is unintentionally missing.



In addition there are some more technical known bugs which have not been dealt with at present but may not be noticable on your machine.

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