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 [log in to unmask] - 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
> [log in to unmask]
> [log in to unmask]
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