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Table 1 Chimera results for difficult structure pairs

From: Tools for integrated sequence-structure analysis with UCSF Chimera

pair PDB ID PDB ID MM-default MM-noSS MM-allSS
1 3chy 2fox 21/1.2, 88/2.2 NR 22/1.1, 88/2.4
2 2aza A 1paz 34/1.2, 79/2.0 8/1.5, 19/2.7 16/1.4, 74/2.3
3 1cew I 1mol A 29/1.0, 73/1.9 6/0.8, 7/1.5 26/0.9, 70/2.0
4 1cid 2rhe 38/1.1, 90/2.0 10/1.3, 21/2.4 11/1.3, 57/2.5
5 1crl 1ede 32/1.3, 184/2.5 6/1.3, 26/3.2 13/1.3, 166/2.6
6 2sim 1nsb A 33/1.2, 257/2.6 4/1.5, 28/3.2 20/1.2, 174/2.9
7 1ten 3hhr B 53/1.1, 82/1.3 4/1.0, 16/2.9 5/0.9, 22/2.9
8 1tie 4fgf 21/1.3, 73/2.2 6/1.1, 22/2.7 15/1.2, 97/2.2
9 2snv 5ptp 32/1.3, 118/2.3 8/1.5, 22/2.4 12/1.4, 103/2.4
10 1gp1 A 2trx A 33/1.0, 89/1.8 5/0.5, 17/2.7 30/1.2, 88/1.7
  1. Results are of the form N/RMSD, where N is the number of residue pairs matched and RMSD is the corresponding alpha-carbon root-mean-square deviation. The first set per column represents the final MatchMaker iteration (after pruning), while the second represents all equivalences from subsequent use of Match -> Align (cutoff 5.0 angstroms). MM-default: MatchMaker with default parameters (BLOSUM-62, 30% secondary structure weighting, prior secondary structure calculation, iteration cutoff 2.0 angstroms; further details are available in the supplementary information [see supplementary.doc]). MM-noSS: same as MM-default except without secondary structure scoring. MM-allSS: same as MM-default except with only the secondary structure term (100% weighting). NR: no results; MatchMaker iteration ended prematurely when the number of residue pairs fell below four.