CE-Symm 2.2.2 gives an error when writing out the symmetry of the N0BET9 AlphaFold model:
runCESymm.sh --simple - -J --rndseed 1 -v AF-N0BET9-F1-model_v4.cif
Structure NumRepeats SymmGroup Reason
272 [main] INFO org.biojava.nbio.structure.align.client.StructureName - Provided structure name 'AF-N0BET9-F1-model_v4.cif' matches file name in directory /Users/bliven_s/Downloads. Will read structure data from file /Users/bliven_s/Downloads/AF-N0BET9-F1-model_v4.cif.
621 [pool-2-thread-1] INFO org.biojava.nbio.structure.symmetry.internal.CeSymm - Open Symmetry detected
632 [pool-2-thread-1] INFO org.biojava.nbio.structure.align.client.StructureName - Provided structure name 'AF-N0BET9-F1-model_v4.cif' matches file name in directory /Users/bliven_s/Downloads. Will read structure data from file /Users/bliven_s/Downloads/AF-N0BET9-F1-model_v4.cif.
632 [pool-2-thread-1] INFO org.biojava.nbio.structure.align.client.StructureName - Provided structure name 'AF-N0BET9-F1-model_v4.cif' matches file name in directory /Users/bliven_s/Downloads. Will read structure data from file /Users/bliven_s/Downloads/AF-N0BET9-F1-model_v4.cif.
1193 [pool-2-thread-1] INFO org.biojava.nbio.structure.symmetry.internal.CeSymm - Open Symmetry detected
1194 [pool-2-thread-1] WARN org.biojava.nbio.structure.symmetry.utils.SymmetryTools - Adding 0 ligands to .A_1-16
1195 [pool-2-thread-1] WARN org.biojava.nbio.structure.symmetry.utils.SymmetryTools - Adding 0 ligands to .A_19-34
1195 [pool-2-thread-1] WARN org.biojava.nbio.structure.symmetry.utils.SymmetryTools - Adding 0 ligands to .A_36-51
1195 [pool-2-thread-1] WARN org.biojava.nbio.structure.symmetry.utils.SymmetryTools - Adding 0 ligands to .A_54-69
1195 [pool-2-thread-1] WARN org.biojava.nbio.structure.symmetry.utils.SymmetryTools - Adding 0 ligands to .A_70-85
1195 [pool-2-thread-1] WARN org.biojava.nbio.structure.symmetry.utils.SymmetryTools - Adding 0 ligands to .A_86-101
1195 [pool-2-thread-1] WARN org.biojava.nbio.structure.symmetry.utils.SymmetryTools - Adding 0 ligands to .A_102-117
1196 [pool-2-thread-1] WARN org.biojava.nbio.structure.symmetry.utils.SymmetryTools - Adding 0 ligands to .A_119-134
1196 [pool-2-thread-1] WARN org.biojava.nbio.structure.symmetry.utils.SymmetryTools - Adding 0 ligands to .A_136-151
1196 [pool-2-thread-1] WARN org.biojava.nbio.structure.symmetry.utils.SymmetryTools - Adding 0 ligands to .A_152-166
1200 [pool-2-thread-1] INFO org.biojava.nbio.structure.cluster.SubunitCluster - SubunitClusters are structurally similar with 0.00 RMSD 0.00 coverage
1201 [pool-2-thread-1] INFO org.biojava.nbio.structure.cluster.SubunitCluster - SubunitClusters are structurally similar with 0.00 RMSD 0.00 coverage
1201 [pool-2-thread-1] INFO org.biojava.nbio.structure.cluster.SubunitCluster - SubunitClusters are structurally similar with 0.00 RMSD 0.00 coverage
1201 [pool-2-thread-1] INFO org.biojava.nbio.structure.cluster.SubunitCluster - SubunitClusters are structurally similar with 0.00 RMSD 0.00 coverage
1201 [pool-2-thread-1] INFO org.biojava.nbio.structure.cluster.SubunitCluster - SubunitClusters are structurally similar with 0.00 RMSD 0.00 coverage
1201 [pool-2-thread-1] INFO org.biojava.nbio.structure.cluster.SubunitCluster - SubunitClusters are structurally similar with 0.00 RMSD 0.00 coverage
1201 [pool-2-thread-1] INFO org.biojava.nbio.structure.cluster.SubunitCluster - SubunitClusters are structurally similar with 0.00 RMSD 0.00 coverage
1201 [pool-2-thread-1] INFO org.biojava.nbio.structure.cluster.SubunitCluster - SubunitClusters are structurally similar with 0.00 RMSD 0.00 coverage
1202 [pool-2-thread-1] INFO org.biojava.nbio.structure.cluster.SubunitCluster - SubunitClusters are structurally similar with 0.00 RMSD 0.00 coverage
1204 [pool-2-thread-1] WARN writers.OutputWriter - Could not write result for entry: AF-N0BET9-F1-model_v4.cif. Writting empty row.
AF-N0BET9-F1-model_v4.cif 10 AF-N0BET9-F1-model_v4.cif 1 C1 Error
1204 [pool-2-thread-1] INFO workers.CeSymmWorker - Finished job: AF-N0BET9-F1-model_v4.cif
1213 [main] INFO main.CeSymmMain - Total runtime: 942, mean runtime: 942
Other seeds (eg --rndseed 2) are successful, but this seems to be just because they don't meet the --minlen=15 requirement so they don't get reported as significant.
CE-Symm 2.2.2 gives an error when writing out the symmetry of the N0BET9 AlphaFold model:
Other seeds (eg
--rndseed 2) are successful, but this seems to be just because they don't meet the--minlen=15requirement so they don't get reported as significant.