dm-averaging

[Jan Abendroth <Jan.Abendroth@uni-koeln.de>]

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Dear crystallographers,
i want to use dm in order to average my map. 
In the asu of my crystal (c2221) there are 6 copies of the protomer
grouped as three dimers. I found out the ncs-operations between the
dimers and within one dimer. I did some few rounds of histogram-matching
and solvent-flattening. Form the bones produced by xdlmapman one could
nicely distinguish the three dimers. So I first want to average the
three dimers taking one dimer as an entity. Therefore I did the
following steps:

1. I edited the bones-pdb-file for one dimer in order to get a decent
ncs-mask.
2. This edited file was converted in a mask with script A (see below)
3. A solvent mask was produced with a quick dm-rund using script B
4. Using the ncs- and solvent-masks from above and the ncs-operators
(the two 2-fold axes from one dimer to each of the to others) I wanted
to run dm for averaging (script C).

Here the program produces a segmentation fault and dumps a core. The
program stops at differnet stages depending on the computer used. Using
a linux pc the program reaches furthest. 
Here dm runs all three cycles, writes the new solvent-mask SOLOUT and
crashes after the statement:
FORMATTED      OLD     file opened on unit   7
 Logical name: SYMOP, Full name: /usr/local/ccp4/lib/data/symop.lib

Even when I skip one or both 2-fold axes the same error occurs. Might it
be a problem of the big unit cell (ca. 120 x 220 x 210 AA)?

Do you have any clue what could have happened? I would be very happy
about any suggestions.

Best regards

Jan



#################
#### SCRIPTS ####
#################

### A ### conversion of pdb to ncs-mask ###
#!/bin/csh -ef 
ncsmask XYZIN dimer.pdb MSKOUT dimer.msk << eof1 | tee ncsmask.log
SYMMETRY c2221
RADIUS 5
AVERAGE 1
ROTATE \
 MATRIX 0 0 0 \
        0 0 0 \
        0 0 0
 TRANSLATE 0 0 0
ROTATE \
 MATRIX  0.51086     0.85768    -0.05839 \
         0.85768    -0.51312    -0.03315 \
        -0.05839    -0.03315    -0.99774
 TRANSLATE -59.35341   109.56364    73.56290
ROTATE \
 MATRIX 0.38851     0.92070     0.03702 \
        0.92070    -0.38950     0.02455 \
        0.03702     0.02455    -0.99901
TRANSLATE -67.47792    94.98884   168.48163
OVERLAP
eof1                                          

### B ### calculation of solvent-mask ###
dm HKLIN solve.mtz HKLOUT dm1.mtz SOLOUT solvent.msk << eof2 | tee
dm-solvmask.log
LABIN FP=FP       SIGFP=SIGFP PHIO=PHIB   FOMO=FOM
LABO  FDM=FDM     PHIDM=PHIDM FOMDM=FOMDM FCDM=FCDM   PHICDM=PHICDM -
      HLADM=HLADM HLBDM=HLBDM HLCDM=HLCD  HLDDM=HLDDM
SOLC .38
MODE solv hist
NCYC auto
COMBINE pert
eof2


### C ### ncs-averaging ###
dm HKLIN solve.mtz    HKLOUT dm_ncs.mtz \
   SOLIN solvent.msk  SOLOUT solvent_dm.msk \
   NCSIN1 dimer.msk   NCSOUT dimer_dm.msk     << eof3 | tee dm.log
LABIN FP=FP       SIGFP=SIGFP PHIO=PHIB   FOMO=FOM
LABO= FDM=FDM     PHIDM=PHIDM  FOMDM=FOMDM FCDM=FCDM PHICDM=PHICDM \
      HLADM=HLADM HLBDM=HLBDM  HLCDM=HLCD  HLDDM=HLDDM
SOLC .38
MODE solv hist aver
NCYC 3
COMBINE pert
AVERAGE refine
  ROTATE MATRIX 0 0 0 0 0 0 0 0 0
  TRANSLATE 0 0 0
AVERAGE refine
  ROTATE MATRIX  0.51086     0.85768    -0.05839 \
                 0.85768    -0.51312    -0.03315 \
                -0.05839    -0.03315    -0.99774
  TRANSLATE -59.35341   109.56364    73.56290
AVERAGE refine
   ROTATE MATRIX 0.38851     0.92070     0.03702 \
                 0.92070    -0.38950     0.02455 \
                 0.03702     0.02455    -0.99901  
   TRANSLATE   -67.47792    94.98884   168.48163
eof3
#############################
-- 
------------------------------
Jan Abendroth
Institut fuer Biochemie
Universitaet Koeln
Zuelpicher Strasse 47
D-50674 Koeln

Tel: +49-(0)221 470 6455 (Labor)
                    6445 (Buero)
Fax: +49-(0)221 470 5092