[ccp4bb]: Multi-body search with AMoRe

[Huiying Li <hli@bragg.bio.uci.edu>]

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Hi,

I am running AMoRe on a two-domain protein using two search models. I used
some scripts that worked well two years ago. There seem to be some changes
ever since in the way AMoRe handling the multi-body search. The CCP4 of
version 4.0.1 is the package we have installed currently on our computers. 

For instance, running ROTING with the second search model, the input
script has to include BOTH table files like:

amore \
TABLE1 ../foe2_model.tab \
TABLE2 spy_ala.tab \
HKLPCK2 search2.hkl \
hklpck0 ../foe2.hkl  \
clmn2 search2.clmn \
clmn0 foe2.clmn  \
> roting.out <<EOF

.......


I recall the older version of AMoRe did not require TABLE1 to be
designated when running ROTING on search model 2.  I wonder if there are  
other changes related to multi-body search that have been implemented in
the current version of AMoRe. I had trouble to get TRAING step running
with an input script that worked well with older version of AMoRe:

amore \
TABLE1 ../foe2_model.tab \
TABLE2 spy_ala.tab \
hklpck0 foe2b.hkl  \
> traing1.out <<EOF

TRAFUN CB NMOL 2 RESO 20 5     -
 PKLIM 0.5  NPIC 10
 HKLM 80 80 80 97
 SYMM P432
 TITLE : Translation function
CRYSTAL ORTH  1 FLIMI 0 10000000   SHARP 0.0
 SOLUTION FIX  1   26.28   68.09  115.08  0.1920  0.9378  0.6464 63.2 39.0
55.4   1
 SOLUTIONRC    2   78.72   52.67   34.00  0.0000  0.0000  0.0000 15.4 59.2
23.4 15.9 1
 SOLUTIONRC    2   37.78   81.01  297.82  0.0000  0.0000  0.0000 15.4 59.2
23.4 16.0 2
 
.........

EOF
#####################################################3
#
fgrep  "SOLUTIONT" traing1.out | sort -r +8 -9 > traing1_cc.list

I had the following error message when I excuted the above script:

<!--SUMMARY_BEGIN-->
 amore:  Use: <logical name> <filename> ...
 amore:  Use: <logical name> <filename> ...                                     
                      
 Times: User:       0.0s System:    0.0s Elapsed:    0:00
<!--SUMMARY_END-->
hklpck0: Command not found.

I don't know where the problem is. Any help would be appreciated.

Huiying Li
--------------------------------------------------
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1797);  Fax: 949-824-3280
email: hli@bragg.bio.uci.edu
--------------------------------------------------