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
IonCom troubleshooting
Re: IonCom troubleshooting
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?
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?
Re: IonCom troubleshooting
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
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