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Hi all,
I am trying to run the helix recognition program 'helreco' within
ARP/wARP using the CCP4i. The process dies with the error messages
attached below.
Any ideas?
Cheers
Jan
here the log files
#####################################
7_helreco.log
~~~~~~~~~~~~~
...
The map has been calculated
... and extended to the unit cell
The density thresholds are set to 1.01 and 10.88
QUITTING ... PROGRAM TO BLAME: HELIX_CALPHAS
*** Look for error message at file: 7_warp_helices_details.log
7_warp_helices_details.log:
~~~~~~~~~~~~~~~~~~~~~~~~~~~
... skipping quite a bit ...
mapmask: (mapmask) - normal termination
Times: User: 0.6s System: 0.1s Elapsed: 0:02
</pre>
</html>
###############################################################################
### ARP/wARP Program Suite: Helix_threshold 1 Jul 2004
O.Kirillova&V.Lamzin #
############ Copyright 1998 European Molecular Biology
Laboratory############
###############################################################################
User: jan Run date and time: Thu Dec 29 11:45:44 2005
Number of atoms: Solvent content: Coefficient:
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: MAPIN Filename:
/Home/jan/linux/xtal-data/2005_12_ALS/blabla/resolve/data/resolve5-inv.ext
File name for input map file on unit 1 :
/Home/jan/linux/xtal-data/2005_12_ALS/blabla/resolve/dat
file size = 8071700 ; logical name MAPIN
Number of columns, rows, sections ............... 171 171 69
Map mode ........................................ 2
Start and stop points on columns, rows, sections 0 170
0 170 0 68
Grid sampling on x, y, z ........................ 170 68 170
Cell dimensions ................................. 84.01100
33.21900 86.26200 90.00000 110.84900 90.00000
Fast, medium, slow axes ......................... Z X Y
Minimum density ................................. -2.44802
Maximum density ................................. 3.18931
Mean density .................................... 0.00008
Rms deviation from mean density ................. 0.06912
Space-group ..................................... 4
Number of titles ................................ 1
Titles :
map calculated with starting phases
Space group number 4 P21
No of symmetry operators 2
1 symmetry matrix (identity matrix) and translation vector:
1.000 0.000 0.000 0.000
0.000 1.000 0.000 0.000
0.000 0.000 1.000 0.000
2 symmetry matrix (2-fold rotation) and translation vector:
-1.000 0.000 0.000 0.000
0.000 1.000 0.000 0.500
0.000 0.000 -1.000 0.000
coef vol frac 1.25 112486.82 12332.3896
frac 0.109634086
cutoffs 1.01 10.88
###############################################################
### CA-trace: Helix_Recognition 19/04/2004 ###
###############################################################
low score predictions included
fragments will be assembled in a molecule
score function 0
the length limit 7
cutoff = 1.010000
cutoff2 = 10.880000
map to be interpreted is
</Home/jan/linux/xtal-data/2005_12_ALS/blabla/resolve/data/resolve5-inv.ext>
output will be written in
</Home/jan/linux/xtal-data/2005_12_ALS/blabla/resolve/data/resolve5-inv.pdb.temp1>
reading the map ...
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name:
/Home/jan/linux/xtal-data/2005_12_ALS/blabla/resolve/data/resolve5-inv.ext
Filename:
/Home/jan/linux/xtal-data/2005_12_ALS/blabla/resolve/data/resolve5-inv.ext
Map characteristics:
MAP Title: map calcul
MAP Space group number 4
MAP Cell parameters 84.011 33.219 86.262 90.000 110.849 90.000
MAP Grid sampling on X, Y, Z 170 68 170
MAP Axes order (fast, medium, slow) Z X Y
MAP Columns (Z) 171 0 170
MAP Rows (X) 171 0 170
MAP Sections (Y) 69 0 68
MAP Density min, max, mean, rms -2.448 3.189 0.000 0.069
Orthogonalisation code 1
Transformation matrix Fract. to orthogonal
84.011002 0.000000 -30.701183
0.000000 33.219002 0.000000
0.000000 0.000000 80.613708
Transformation matrix Orthogonal to fract.
0.011903 0.000000 0.004533
0.000000 0.030103 0.000000
0.000000 0.000000 0.012405
Space group number 4 P21
No of symmetry operators 2
1 symmetry matrix (identity matrix) and translation vector:
1.000 0.000 0.000 0.000
0.000 1.000 0.000 0.000
0.000 0.000 1.000 0.000
2 symmetry matrix (2-fold rotation) and translation vector:
-1.000 0.000 0.000 0.000
0.000 1.000 0.000 0.500
0.000 0.000 -1.000 0.000
read_map2: points in too high density: 64
the map has been read
now the map extension ... done
neighbour arrays have been made
neighbours have been found
sorting neighbours ... done
constructing sets of 3 points ... done
constructing sets of 4 points ... done
constructing sets of 5 points ... done
preparing for chain formation ... done
forming chains ...
(... here the log file ends abruptly ...)
