Dear Jonathan
this sounds like a known issue with the version on molrep that was
released with ccp4 version 6.1.1 (so if you are having the problem
with 6.1.3 then it has got back in). For some reason we did not get
to the bottom of the file path gets doubled up, /home/caruthej/bo3/
ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/
bo3P1_11_molrep_trfn_scr.crd , we have the /home twice. The
suggested work around is to upgrade to 6.1.3 . If you do not wish to
upgrade fully at this point just download the new version and replace
the molrep in $CCP4/bin
Sorry for the problem
Charles Ballard
CCP4
On 26 Feb 2010, at 19:31, Jonathan Marvin Caruthers wrote:
All:
Can anyone help me out here? I'm trying to get Molrep to run but
it seems to be crashing while trying to open some file after it's
done the rotation function search. I'm getting the following error:
**************************************************************
Number of RF peaks : 30
theta phi chi alpha beta gamma
Rf Rf/sigma
Sol_RF 1 44.61 -44.03 112.01 272.52 71.21 180.58
0.3240E+05 10.69
Sol_RF 2 62.99 136.68 133.64 93.36 109.98 0.00
0.3154E+05 10.40
Sol_RF 3 111.50 -133.69 138.32 92.40 120.82 179.79
0.2804E+05 9.25
Sol_RF 4 139.89 46.56 102.16 273.12 60.17 0.00
0.2556E+05 8.43
Sol_RF 5 147.85 44.94 96.78 271.31 46.89 1.43
0.1701E+05 5.61
Sol_RF 6 119.97 -108.35 162.70 88.58 117.83 125.29
0.1673E+05 5.52
Sol_RF 7 56.80 141.24 140.27 107.82 103.81 5.34
0.1650E+05 5.44
Sol_RF 8 55.15 142.30 142.33 111.46 101.91 6.87
0.1601E+05 5.28
Sol_RF 9 54.36 143.15 143.09 113.35 100.88 7.05
0.1563E+05 5.16
Sol_RF 10 115.41 -108.41 160.88 93.02 125.92 129.84
0.1562E+05 5.15
Sol_RF 11 55.10 137.38 127.36 96.53 94.64 1.77
0.1554E+05 5.13
Sol_RF 12 142.36 34.36 113.03 254.24 61.23 5.51
0.1539E+05 5.08
Sol_RF 13 115.81 -141.38 155.86 64.78 123.37 167.54
0.1516E+05 5.00
Sol_RF 14 147.45 78.25 143.98 279.34 61.55 302.85
0.1501E+05 4.95
Sol_RF 15 116.29 -141.01 153.70 66.80 121.63 168.82
0.1500E+05 4.95
Sol_RF 16 75.23 164.12 119.33 97.66 113.14 309.42
0.1461E+05 4.82
Sol_RF 17 150.03 57.40 91.74 285.64 42.03 350.83
0.1450E+05 4.78
Sol_RF 18 49.18 -35.04 85.65 266.17 61.92 156.24
0.1437E+05 4.74
Sol_RF 19 139.72 66.72 124.31 281.42 69.74 327.98
0.1434E+05 4.73
Sol_RF 20 60.59 -24.12 79.57 268.13 67.75 136.36
0.1434E+05 4.73
Sol_RF 21 118.54 -105.41 168.98 86.00 121.95 116.82
0.1429E+05 4.71
Sol_RF 22 109.08 -138.84 156.70 73.40 135.51 171.08
0.1422E+05 4.69
Sol_RF 23 37.48 -33.22 75.56 268.37 43.78 154.81
0.1417E+05 4.67
Sol_RF 24 118.00 -105.87 171.24 83.39 123.37 115.14
0.1411E+05 4.65
Sol_RF 25 119.13 -105.81 169.16 85.22 120.83 116.84
0.1410E+05 4.65
Sol_RF 26 117.07 -130.56 136.98 90.32 111.87 171.45
0.1403E+05 4.63
Sol_RF 27 142.78 18.10 126.65 230.35 65.43 14.15
0.1400E+05 4.62
Sol_RF 28 135.68 14.72 139.96 221.71 82.06 12.27
0.1399E+05 4.62
Sol_RF 29 146.60 71.15 139.06 275.24 62.10 312.94
0.1397E+05 4.61
Sol_RF 30 58.45 -20.76 81.24 273.41 67.39 134.93
0.1392E+05 4.59
Final number of peaks : 30
INFO: Relations between peaks see in molrep.doc
NCS_model (from Model Self rotation Function): 1
Program will use NCS =: 1
Sol_
Sol_--- Multi-copy Search ---
Sol_
Sol_ Resmin,Resmax : 77.32 4.00
Sol_ Radius_giration : 30.442
Radius_max : 56.282
Sol_ Chi,Delta : 0.000 10.000
Sol_ Dist_min,max,Dpar_max : 30.442 1000.000 1000.000
Sol_
Sol_--- First monomer search ---
Sol_
Sol_ RF TF Tf/sig TFcntrst PKind PKmax PKmin Rfac Scor
Scor_max Cntrst
Open failed: Unit: 8, File: /home/caruthej/bo3/ccp4/
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/
bo3P1_11_molrep_trfn_scr.crd (logical: /home/caruthej/bo3/ccp4/
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd)
MOLREP(ccp4): Open failed: File: /home/caruthej/bo3/ccp4/
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd
Times: User: 82.2s System: 1.2s Elapsed: 1:35
</pre>
</html>
**********************************************************************
*****
* Information from CCP4Interface script
**********************************************************************
*****
The program run with command: /usr/local/ccp4-6.1.0/ccp4-6.1.0/bin/
molrep PATH_SCR "/home/caruthej/bo3/ccp4/bo3P1_11_molrep_" PATH_OUT
"/home/caruthej/bo3/ccp4/bo3P1_11_molrep_" HKLIN "/home/caruthej/
bo3/P1/ccp4/merged.mtz" MODEL "/home/caruthej/bo3/P1/cns/model.pdb"
has failed with error message
Last system error message: No such file or directory
MOLREP(ccp4): Open failed: File: /home/caruthej/bo3/ccp4/
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd
**********************************************************************
*****
#CCP4I TERMINATION STATUS 0 "Last system error message: No such
file or directory MOLREP(ccp4): Open failed: File: /home/
caruthej/bo3/ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/
bo3P1_11_molrep_trfn_scr.crd "
#CCP4I TERMINATION TIME 26 Feb 2010 11:34:11
#CCP4I MESSAGE Task failed
*************************************************************
It appears to be trying to open some kind of file necessary to
perform the translation function, but I can't get any hits even
googling up "molrep_trfn_scr.crd" to figure out what that file is
all about, what it means, and why Molrep needs it. If anybody
familiar with Molrep out there can help me out, it would be greatly
appreciated. We recently upgraded our machines here and some
things were shifted around and I've been chasing bugs ever since so
it wouldn't surprise me if something got moved or if there's some
problem with my path so that Molrep can no longer find this file,
or if there's some permissions error so it can't write it out or
something along those lines, but if anyone out there knows a little
more about what's going on and is willing to help me out, please
feel free to post a solution to the board, or to contact me
directly at caruth...@mac.com - the latter being the best way to
get me. Thanks in advance for any help anyone can provide.
Sincerely,
Jon Caruthers
Stowell Lab
University of Colorado
caruth...@mac.com
jonathan.caruth...@colorado.edu
