My (educated) guess is that Coot doesnt recognise your nucleotides as such and hence doesnt find any atoms to do the lsq superposition with. The different nucleotide name 'conventions' strike again....
B *************************************************** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487673 fax: (+46) 08-327626 email: [email protected] ----- Original Message ----- From: Francis E Reyes <[email protected]> Date: Thursday, September 24, 2009 4:54 pm Subject: [COOT] NCS ghosts and map broken? To: [email protected] > Hi all > > It seems that adding ncs ghosts and then ncs maps is broken for my > model / coot combo. > > Coot is at ver 0.6-pre-1 rev 2334. > > Thanks! > > > > > > > This is what phenix.simple_ncs_from_pdb gives me > ==================== Process input NCS or/and find new NCS > ==================== > > NCS groups found in parameter file: 1 > NCS group 0: > reference= chain A and (resseq 1:39 or resseq 43:54 ) > selection= chain B and (resseq 1:39 or resseq 43:54 ) > > Automatic NCS search: > > > # simple_ncs_from_pdb > # > # Find ncs among chains in a PDB file > > # type phenix.doc for help > > Getting NCS from suggested chains: > RMSD for suggested group ['A', 'B'] [[[1, 39], [43, 54]], [[1, > 39], > [43, 54]]] is 0.0121907468281 > > Updated/new NCS groups: > refinement.ncs.restraint_group { > reference = chain 'A' and (resseq 1:39 or resseq 43:54 ) > selection = chain 'B' and (resseq 1:39 or resseq 43:54 ) > } > > > ----------Building NCS restraints---------- > > NCS restraint group 1: > NCS operator 1: > Reference selection: "chain A and (resseq 1:39 or resseq 43:54 )" > Other selection: "chain B and (resseq 1:39 or resseq 43:54 )" > Number of atom pairs: 1103 > Rotation={{-0.500763, -0.865584, 0.000393409}, > {-0.865584, 0.500763, 0.000526561}, > {-0.000652788, -7.68463*^-05, -1}} > Translation={{-53.5412}, {-30.8968}, {104.68}} > Histogram of differences: > 0.000454 - 0.008521: 479 > 0.008521 - 0.016588: 422 > 0.016588 - 0.024655: 146 > 0.024655 - 0.032722: 40 > 0.032722 - 0.040790: 13 > 0.040790 - 0.048857: 3 > RMS difference with respect to the reference: 0.013137 > > > > > However when I try to overlay ncs ghosts and a ncs map I get this > from > coot > NCS_controller display chain toggled for imol 0 chain 1 state 1 > %%%% ncs_control_display_chain > There are 1 ghosts > ighost: 0 > name: "NCS found from matching Chain B onto Chain A" > chainid: B > target chain id: A > display_it_flag 1 > %%%%%%%%% calling fill_ghost_info() from c-interface.cc > make_ncs_ghosts_maybe() > INFO:: NCS chain comparison 51/51 > First atom of 1103 in first selection 1/A/1/Gr/ P altLoc :: > segid :A: pos: (-26.744,-11.257,24.195) B-factor: 106.43 > First atom of 1103 in second selection 1/B/1/Gr/ P altLoc :: > segid :A: pos: (-30.371,-13.357,80.514) B-factor: 107.38 > WARNING - no residue for reference residue number 40 A > WARNING - no residue for moving molecule residue number 40 B > WARNING - no residue for reference residue number 41 A > WARNING - no residue for moving molecule residue number 41 B > WARNING - no residue for reference residue number 42 A > WARNING - no residue for moving molecule residue number 42 B > WARNING:: no points to do matching > find_ncs_matrix returns (LSQ) junk > | 0, 0, 0| > | 0, 0, 0| > | 0, 0, 0| > ( 0, 0, 0) > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" > INFO:: installing ghost map with name :NCS found from matching > Chain B > onto Chain A > Done install_ghost_map > Reference matcher: 0 and 0 > |6.953e-310,6.953e-310,6.953e-310| > |2.238e-314, 1.16e-315,1.334e-322| > |4.244e-314,4.032e-321, 0| > (2.144e-314, 0, 0) > inverse of reference matcher transformation: > | nan, nan, nan| > | nan, nan, nan| > | nan, nan, nan| > ( nan, nan, nan) > boxing over uvw = ( -0.6365, -0.3535, 0.08703) to uvw = > ( 0.2349, 0.1764, 0.6158) > INFO:: There were 2 maps contributing to the average > INFO:: rescaling by 0.5 > INFO:: 316520 out of 331872 (95.3741%) map points were masked out > of > NCS average target volume, chain A > INFO:: made 1 averaged map(s) > Map statistics: mean: nan st.d: nan > Map statistics: min: 0, max: 0 > /sw/bin/coot: line 5: 66873 Segmentation fault /sw64/bin/coot- > real "$@" > > > > > > > --------------------------------------------- > Francis Reyes M.Sc. > 215 UCB > University of Colorado at Boulder > > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D >
