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Eugenere - are you responsible for mmdb? Could these features cause problems? Eleanor The PDB file Thern_tRNA has some anomalies - 1) several unneeded TER cards TER 399 LYS A 52 - there is a chain break here but not a chain termination TER 3219 GLY A 421 TER 3343 GTP C -1 - Never sure about these but GTP is not part of chain TER 4163 G C 37 TER 4967 A C 76 2) Some of the atom types are unusual eg N1+ here instead of N I am not sure whether that is important of not. ATOM 22 NH1 ARG A 4 24.496 181.121 132.218 1.00103.17 N1+ ANISOU 22 NH1 ARG A 4 15732 10019 13448 1911 785 -419 N1+ On 10 September 2018 at 10:36, Eleanor Dodson <[log in to unmask]> wrote: > Charlie - I will try to check this, but cant read your pse file - can you > find another format? > > Thanks Eleanor > > On 8 September 2018 at 12:28, Carter, Charlie <[log in to unmask]> wrote: > >> Hi folks, >> >> I continue to use lsqkab because it offers unique flexibility and >> features appropriate to what I do. >> >> Currently, I’ve a project that requires such superposition and for that I >> created from the original pdb files a set of monomeric pdb files that have >> already been superposed by POSA. The POSA alignment used all the residues, >> and I want to orient only a subset that is structurally invariant, in order >> to identify possible interdomain motions. >> >> There are ten such files; eight appear to work properly and have aligned. >> The other two give one or another of two pathologies. The first appears >> simply to get confused and output a rotated coordinate file that appears to >> be ~90 degrees off, despite the fact that the residue numbering is correct >> (see attached .pse file in which three _Urz coordinate sets are >> illustrated, which were superimposed on Ecoli_Urz. The Ttherm_H file is >> correctly rotated; the Stau_LF file is not.). >> >> I decided to try to rotate the two files into an intermediate orientation >> that gave a satisfactory result, i.e. Ttherm_H. The first attempt at this >> involved a second problematic file, Ttherm_tRNA. LSQKSB gave the following >> error message, which instructs me to contact the developers. The >> problematic pdb file, Ttherm_tRNA.pdb, is also attached. >> >> >> * *** RWBROOK error: point code unit function* >> * *** 1 -102 2 MMDB_F_Atom* >> * *** file : Ttherm_tRNA_rot.pdb* >> * *** reason : internal error #2 -- report to developer* >> * *** Execution stopped.* >> >> I should note that I am still using the following version of the software: >> >> source /usr/local/bin/ccp4-7.0/include/ccp4.setup >> >> The commands in my script are: >> >> #source /usr/local/bin/ccp4-7.0/include/ccp4.setup >> lsqkab XYZINM $1 XYZINF $2 XYZOUT $1_rot.pdb << END-lsqkab >> FIT RESIDUE MAIN 8 TO 82 >> MATCH 10 to 84 >> FIT RESIDUE MAIN 83 TO 111 >> MATCH 85 to 113 >> FIT RESIDUE MAIN 122 TO 129 >> MATCH 124 to 131 >> OUTPUT XYZ >> END >> END-lsqkab >> >> Many thanks in advance for any help. >> >> >> >> > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1