Dear list, I'm trying to undestand the NCS symmetry in a unit cell with 8 molecules (2 A resolution). The unit cell is almost orthorhombic (68.900 79.240 90.040 89.97 90.04 89.97), but only P1 + twinning worked for MR and for refining the structure (Rfree=0.22; Rcryst=0.18). The crystal simulated a P222 space group (the best seemed to be P21212), so I'd expect NCS axis parallel to . Now I've used phenix.simple_ncs_from_pdb to get the symmtery operators (see ouput below). I've read the manual, but I'm nevertheless finding it difficult to " see" the NCS axis. Any suggestions, please, on how to interpret the output, please, and "draw" the axis or on any alternatives on how to proceed? Many many thanks and a huge apology for the naive question (this is only my third strutcure...). Claudia --------------------------------------------------------------------------- # simple_ncs_from_pdb # # Find ncs among chains in a PDB file # type simple_ncs_from_pdb --help for help Parameters used for simple_ncs_from_pdb: find_ncs { temp_dir = "" min_length = 10 njump = 1 njump_recursion = 10 min_length_recursion = 50 min_percent = 95 max_rmsd = 2 quick = True max_rmsd_user = 3 domain_finding_parameters { find_invariant_domains = True initial_rms = 0.5 match_radius = 2 similarity_threshold = 0.75 smooth_length = 0 min_contig_length = 3 min_fraction_domain = 0.2 max_rmsd_domain = 2 } verbose = False } Chains in this PDB file: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'] GROUPS BASED ON QUICK COMPARISON: [['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']] Looking for invariant domains for ...: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'] [[[19, 130], [148, 253]], [[21, 130], [148, 253]], [[21, 130], [148, 253]], [[19, 128], [149, 253]], [[19, 130], [148, 253]], [[21, 128], [148, 253]], [[19, 130], [149, 253]], [[21, 129], [149, 253]]] GROUP 1 Summary of NCS group with 8 operators: ID of chain/residue where these apply: [['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'], [[[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]]]] RMSD (A) from chain A: 0.0 0.46 0.47 0.53 0.54 0.48 0.48 0.59 Number of residues matching chain A:[213, 212, 212, 211, 212, 210, 213, 211] Source of NCS info: sortwaterxyzout.pdb OPERATOR 1 CENTER: 19.3475 -10.7352 7.9738 ROTA 1: 1.0000 0.0000 0.0000 ROTA 2: 0.0000 1.0000 0.0000 ROTA 3: 0.0000 0.0000 1.0000 TRANS: 0.0000 0.0000 0.0000 OPERATOR 2 CENTER: 53.8092 24.2127 11.0612 ROTA 1: 0.9998 0.0043 -0.0190 ROTA 2: 0.0045 -0.9999 0.0114 ROTA 3: -0.0190 -0.0115 -0.9998 TRANS: -34.3014 13.1765 20.2795 OPERATOR 3 CENTER: 55.6227 -15.2644 6.2461 ROTA 1: -0.9928 -0.0019 -0.1198 ROTA 2: -0.0045 -0.9986 0.0530 ROTA 3: -0.1197 0.0532 0.9914 TRANS: 75.3327 -25.9880 9.2016 OPERATOR 4 CENTER: 21.4489 28.7297 12.8232 ROTA 1: -0.9923 0.0066 0.1235 ROTA 2: -0.0001 0.9985 -0.0545 ROTA 3: -0.1236 -0.0541 -0.9909 TRANS: 38.7377 -38.6213 24.9897 OPERATOR 5 CENTER: 33.2332 16.3336 52.0552 ROTA 1: 0.9959 0.0207 -0.0884 ROTA 2: -0.0168 0.9988 0.0450 ROTA 3: 0.0892 -0.0433 0.9951 TRANS: -9.4176 -28.8046 -46.0499 OPERATOR 6 CENTER: 35.8216 -23.2140 56.1297 ROTA 1: -0.9985 -0.0249 -0.0490 ROTA 2: -0.0273 0.9985 0.0479 ROTA 3: 0.0477 0.0492 -0.9976 TRANS: 57.2101 10.9031 63.4545 OPERATOR 7 CENTER: 70.2188 11.8599 54.2973 ROTA 1: -0.9987 0.0207 0.0473 ROTA 2: -0.0234 -0.9981 -0.0569 ROTA 3: 0.0460 -0.0580 0.9973 TRANS: 86.6599 5.8364 -48.7180 OPERATOR 8 CENTER: 67.5293 -27.9008 58.5120 ROTA 1: 0.9959 -0.0146 0.0888 ROTA 2: -0.0120 -0.9995 -0.0303 ROTA 3: 0.0892 0.0291 -0.9956 TRANS: -53.5269 -35.9247 61.0251 NCS operators written in format for resolve to: simple_ncs_from_pdb.resolve NCS operators written in format for phenix.refine to: simple_ncs_from_pdb.ncs NCS written as ncs object information to: simple_ncs_from_pdb.ncs_spec Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE