Hi all,
I am trying to run essens. According to the manual, a mask is optional,
especially if you don't know where the protein molecule is. Regardless if
I run it interactively or batch, I get the same error.
Here is my batch file:
#!/bin/csh -f
cd /w1/robert/methylase
/w1/apps/uppsala/rave/6d_essens -b << EOF >& RsrI_meth.log
solve.ccp4
/w1/apps/uppsala/rave/essens_alpha.pdb
yes euler
18 value of k
0.001 cut-off
score_RsrI_meth.E
display_RsrI_meth.E
RsrI_meth.rot
EOF
=========================================================
=========================================================
Here is the log file (minus non-essential text):
Allocate maps of size : ( 10000000)
Allocate masks of size : ( 5000000)
Max nr of atoms : ( 10000)
Input CCP4 map file ? ( )
Input CCP4 map file : (solve.ccp4)
Read header
Input map : (solve.ccp4)
FORMATTED OLD file opened on unit 11
Logical name: solve.ccp4, Full name: solve.ccp4
(Q)QOPEN allocated # 1
User: robert Logical Name: solve.ccp4
Status: READONLY Filename: solve.ccp4
File name for input map file on unit 11 : solve.ccp4
file size = 526336 ; logical name
solve.ccp4
Number of columns, rows, sections ............... 72 96 19
Map mode ........................................ 2
Start and stop points on columns, rows, sections 0 71 0
95 0 18
Grid sampling on x, y, z ........................ 96 144 72
Cell dimensions ................................. 71.24000
130.88000 67.17000 90.00000 90.00000 90.00000
Fast, medium, slow axes ......................... Y X Z
Minimum density ................................. -3.96500
Maximum density ................................. 6.57700
Mean density .................................... -0.00121
Rms deviation from mean density ................. 1.00000
Space-group ..................................... 1
Number of titles ................................ 1
Titles :
Created by MAPMAN V. 980715/5.4.2 at Thu Sep 3 11:42:21 1998 for
user robert
Parameters as read from the map file
Origin ...................... 0 0 0
Extent ...................... 96 72 19
Grid ........................ 96 144 72
Cell axes ................... 71.24 130.88 67.17
Cell angles ................. 90.00 90.00 90.00
UVW (fast, medium, slow) .... Y X Z
Header done
Not in core
Reading levels
Level number : ( 10)
Map read OK
Closing BINARY CCP4 map on unit : ( 11)
Cell axes (A) : ( 71.240 130.880 67.170)
Cell angles (d) : ( 90.000 90.000 90.000)
Grid axes (pts) : ( 96 144 72)
Origin (pts) : ( 0 0 0)
Extent (pts) : ( 96 72 19)
Grid spacing (A): ( 0.742 0.909 0.933)
Mask is *OPTIONAL* !
Input O/MAMA mask file ? ( )
Input O/MAMA mask file : ( )
No mask file provided - use all points in map
Name of template PDB file ? (alpha.pdb)
Name of template PDB file : (/w1/apps/uppsala/rave/essens_alpha.pdb)
Number of atoms : ( 25)
Nr of H stripped : ( 0)
Centre of gravity of atoms : ( 0.000 0.000 0.000)
Using central CA atom as pivot point
Atom : (ATOM 12 CA ALA 3 1.948 -1.374 -1.538 1.00 20.00 6)
Pivot point : ( 1.948 -1.374 -1.538)
Furthest atom (A): ( 6.910)
Safety border X/Y/Z = 11 9 9
Rotations may be in Euler or Polar angles
Use Euler angles (Y/N) ? (Y)
Rotations are Euler angles in degrees
Rotation ALPHA start, end, step ? ( 0.000 359.000 10.000)
Rotation BETA start, end, step ? ( 0.000 179.000 10.000)
Rotation GAMMA start, end, step ? ( 0.000 359.000 10.000)
Rotation ALPHA start, end, step : ( 0.000 359.000 10.000)
Rotation BETA start, end, step : ( 0.000 179.000 10.000)
Rotation GAMMA start, end, step : ( 0.000 359.000 10.000)
Number of rotations : ( 26011)
K = Nr of atoms to sum in K-minimum sum function
Value of K ? ( 15)
K : ( 18)
Minimum density in input map : ( -3.965E+00)
Lower density cut-off ? ( -3.965E+00)
Lower density cut-off : ( 1.000E-03)
Grid points in map : ( 131328)
Grid points >= cut-off : ( 63041)
Output score map file ? (score.E)
Output score map file : (score_RsrI_meth.E)
Output display map file ? (display.E)
Output display map file : (display_RsrI_meth.E)
Output rotation file ? (temp.rot)
Output rotation file : (RsrI_meth.rot)
STOP ... Toodle pip ... statement executed
Initialising output map ...
Determining safety borders ...
Safety border X/Y/Z = 11 9 9
CPU total/user/sys : 4.1 4.0 0.1
Setting up mask ...
(Z) ... 10 0 9 18 10
9
ERROR --- User mask does not overlap with central map region
Can someone explain why I am getting a mask error when I don't want to use
a mask. I want essens to search the whole map. The map was generated by
SOLVE in EZD format and converted to CCP4 format using MAPMAN.
Thanks,
Robert Scavetta
Department of Pharmacology
University of Colorado Health Science Center
Denver, Colorado
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