> What's the 'proper' way to name nucleotides in Coot? (RNA) Well, it's actually mmdb which is handling the nucleotide names in this case. From what I can see the following residue names are recognised as nucleotides (*):
"A", "C", "G", "I", "T", "U", "+A", "+C", "+G", "+I", "+T", "+U", "DA", "DC", "DG", "DI", "DT", "DU", "RA", "RC", "RG", "RU", "5NC", "TYD" Hope this helps, B (*) may depend on version, this is for version 1.19 and 1.21 > On Sep 24, 2009, at 9:43 AM, Bernhard Lohkamp wrote: > > > > > 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 > >> > > --------------------------------------------- > 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 > *************************************************** 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]
