IonCom troubleshooting

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Moderator: robpearc

mascheier
Posts: 2
Joined: Wed May 19, 2021 7:37 pm

IonCom troubleshooting

Post by mascheier »

Dear Zhang Lab Team,

I was trying to run the standalone version of the IonCom. I believe I have the correct setup including I-TASSER5.1 and the libraries but do not have any troubleshooting skills or that much experience coding.
Upon running IonCom I received:
(base) mascheier@123:~$ IonCom_standalone/run_IonCom.pl
job: P3B
begin new job
PDB2Seq failed

Any ideas where to start resolving the issue?

I have also attempted to use the online service job number:
Tips

job 7894 is running
robpearc
Posts: 40
Joined: Sun May 02, 2021 5:49 pm

Re: IonCom troubleshooting

Post by robpearc »

Hello,

Currently, we are catching up on some of the back logged jobs from when the server was down, so we have been experiencing delays for our online server. It seems the error should be with the PDB file you input to the program as PDB2Seq failed to extract the amino acid sequence from the PDB. Would you be able to attach the PDB your input to the program?
mascheier
Posts: 2
Joined: Wed May 19, 2021 7:37 pm

Re: IonCom troubleshooting

Post by mascheier »

Code: Select all

ATOM      1  N   MET B 277      70.211 132.207  13.879  1.00172.98           N  
ATOM      2  CA  MET B 277      71.571 132.782  14.016  1.00172.98           C  
ATOM      3  C   MET B 277      71.530 134.262  14.154  1.00172.98           C  
ATOM      4  O   MET B 277      70.508 134.901  13.897  1.00172.98           O  
ATOM      5  CB  MET B 277      72.383 132.460  12.748  1.00172.98           C  
ATOM      6  CG  MET B 277      73.831 132.954  12.766  1.00172.98           C  
ATOM      7  SD  MET B 277      74.673 132.834  11.160  1.00172.98           S  
ATOM      8  CE  MET B 277      74.472 131.035  11.018  1.00172.98           C  
ATOM      9  N   GLY B 278      72.691 134.801  14.567  1.00 67.14           N  
ATOM     10  CA  GLY B 278      72.975 136.174  14.839  1.00 67.14           C  
ATOM     11  C   GLY B 278      74.380 136.118  15.326  1.00 67.14           C  
ATOM     12  O   GLY B 278      75.258 135.621  14.622  1.00 67.14           O  
ATOM     13  N   ARG B 279      74.650 136.629  16.540  1.00239.96           N  
ATOM     14  CA  ARG B 279      75.990 136.458  17.006  1.00239.96           C  
ATOM     15  C   ARG B 279      76.150 134.981  17.133  1.00239.96           C  
ATOM     16  O   ARG B 279      75.225 134.288  17.554  1.00239.96           O  
ATOM     17  CB  ARG B 279      76.269 137.064  18.393  1.00239.96           C  
ATOM     18  CG  ARG B 279      76.099 138.583  18.457  1.00239.96           C  
ATOM     19  CD  ARG B 279      74.642 139.034  18.574  1.00239.96           C  
ATOM     20  NE  ARG B 279      74.379 139.306  20.017  1.00239.96           N  
ATOM     21  CZ  ARG B 279      74.003 138.296  20.854  1.00239.96           C  
ATOM     22  NH1 ARG B 279      73.865 137.025  20.376  1.00239.96           N1+
ATOM     23  NH2 ARG B 279      73.768 138.557  22.173  1.00239.96           N  
ATOM     24  N   GLY B 280      77.319 134.444  16.745  1.00154.47           N  
ATOM     25  CA  GLY B 280      77.443 133.021  16.828  1.00154.47           C  
ATOM     26  C   GLY B 280      78.867 132.683  17.098  1.00154.47           C  
ATOM     27  O   GLY B 280      79.771 133.486  16.873  1.00154.47           O  
ATOM     28  N   TYR B 281      79.085 131.453  17.596  1.00291.31           N  
ATOM     29  CA  TYR B 281      80.400 130.983  17.898  1.00291.31           C  
ATOM     30  C   TYR B 281      80.578 129.761  17.058  1.00291.31           C  
ATOM     31  O   TYR B 281      79.664 128.948  16.930  1.00291.31           O  
ATOM     32  CB  TYR B 281      80.550 130.585  19.377  1.00291.31           C  
ATOM     33  CG  TYR B 281      81.945 130.125  19.617  1.00291.31           C  
ATOM     34  CD1 TYR B 281      82.953 131.041  19.813  1.00291.31           C  
ATOM     35  CD2 TYR B 281      82.242 128.784  19.662  1.00291.31           C  
ATOM     36  CE1 TYR B 281      84.243 130.625  20.040  1.00291.31           C  
ATOM     37  CE2 TYR B 281      83.530 128.361  19.889  1.00291.31           C  
ATOM     38  CZ  TYR B 281      84.532 129.282  20.077  1.00291.31           C  
ATOM     39  OH  TYR B 281      85.855 128.851  20.310  1.00291.31           O  
ATOM     40  N   PRO B 282      81.719 129.619  16.449  1.00197.44           N  
ATOM     41  CA  PRO B 282      81.904 128.475  15.604  1.00197.44           C  
ATOM     42  C   PRO B 282      81.979 127.221  16.404  1.00197.44           C  
ATOM     43  O   PRO B 282      82.630 127.214  17.447  1.00197.44           O  
ATOM     44  CB  PRO B 282      83.145 128.771  14.767  1.00197.44           C  
ATOM     45  CG  PRO B 282      83.152 130.309  14.676  1.00197.44           C  
ATOM     46  CD  PRO B 282      82.460 130.774  15.969  1.00197.44           C  
ATOM     47  N   HIS B 283      81.322 126.145  15.934  1.00272.56           N  
ATOM     48  CA  HIS B 283      81.371 124.911  16.654  1.00272.56           C  
ATOM     49  C   HIS B 283      80.694 123.891  15.801  1.00272.56           C  
ATOM     50  O   HIS B 283      80.180 124.206  14.729  1.00272.56           O  
ATOM     51  CB  HIS B 283      80.637 124.966  18.007  1.00272.56           C  
ATOM     52  CG  HIS B 283      80.897 123.770  18.875  1.00272.56           C  
ATOM     53  CD2 HIS B 283      80.157 122.643  19.068  1.00272.56           C  
ATOM     54  ND1 HIS B 283      82.018 123.621  19.662  1.00272.56           N  
ATOM     55  CE1 HIS B 283      81.903 122.421  20.285  1.00272.56           C  
ATOM     56  NE2 HIS B 283      80.790 121.791  19.956  1.00272.56           N  
ATOM     57  N   GLY B 284      80.698 122.625  16.253  1.00128.63           N  
ATOM     58  CA  GLY B 284      80.041 121.592  15.513  1.00128.63           C  
ATOM     59  C   GLY B 284      78.590 121.939  15.479  1.00128.63           C  
ATOM     60  O   GLY B 284      77.919 121.765  14.463  1.00128.63           O  
ATOM     61  N   ARG B 285      78.066 122.441  16.613  1.00247.06           N  
ATOM     62  CA  ARG B 285      76.682 122.799  16.684  1.00247.06           C  
ATOM     63  C   ARG B 285      76.640 124.283  16.832  1.00247.06           C  
ATOM     64  O   ARG B 285      77.582 124.889  17.340  1.00247.06           O  
ATOM     65  CB  ARG B 285      75.963 122.193  17.901  1.00247.06           C  
ATOM     66  CG  ARG B 285      75.979 120.662  17.909  1.00247.06           C  
ATOM     67  CD  ARG B 285      75.353 120.048  19.163  1.00247.06           C  
ATOM     68  NE  ARG B 285      75.442 118.567  19.030  1.00247.06           N  
ATOM     69  CZ  ARG B 285      76.580 117.918  19.413  1.00247.06           C  
ATOM     70  NH1 ARG B 285      77.638 118.628  19.904  1.00247.06           N1+
ATOM     71  NH2 ARG B 285      76.664 116.560  19.304  1.00247.06           N  
ATOM     72  N   GLY B 286      75.547 124.917  16.368  1.00143.97           N  
ATOM     73  CA  GLY B 286      75.482 126.342  16.477  1.00143.97           C  
ATOM     74  C   GLY B 286      74.127 126.713  16.978  1.00143.97           C  
ATOM     75  O   GLY B 286      73.155 125.982  16.793  1.00143.97           O  
ATOM     76  N   GLY B 287      74.044 127.886  17.635  1.00146.47           N  
ATOM     77  CA  GLY B 287      72.801 128.373  18.155  1.00146.47           C  
ATOM     78  C   GLY B 287      72.221 129.272  17.117  1.00146.47           C  
ATOM     79  O   GLY B 287      72.609 129.218  15.951  1.00146.47           O  
ATOM     80  N   GLY B 288      71.265 130.133  17.518  1.00145.03           N  
ATOM     81  CA  GLY B 288      70.686 131.004  16.543  1.00145.03           C  
ATOM     82  C   GLY B 288      70.242 132.262  17.215  1.00145.03           C  
ATOM     83  O   GLY B 288      70.013 132.303  18.423  1.00145.03           O  
ATOM     84  N   MET B 289      70.114 133.328  16.403  1.00313.50           N  
ATOM     85  CA  MET B 289      69.672 134.623  16.806  1.00313.50           C  
ATOM     86  C   MET B 289      68.545 134.980  15.889  1.00313.50           C  
ATOM     87  O   MET B 289      68.266 134.290  14.910  1.00313.50           O  
ATOM     88  CB  MET B 289      70.740 135.721  16.697  1.00313.50           C  
ATOM     89  CG  MET B 289      70.357 137.016  17.416  1.00313.50           C  
ATOM     90  SD  MET B 289      70.374 136.892  19.231  1.00313.50           S  
ATOM     91  CE  MET B 289      69.872 138.613  19.524  1.00313.50           C  
TER   
END
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