Hmm - when I try to read Therm_tRNA into the CCP4I2 GUI it says
Cordinate file failed vaildation test! Not sure what that test is but will ask around.. e On 10 September 2018 at 12:15, Carter, Charlie <car...@med.unc.edu> wrote: > Eleanor, > > I’ll check into the tRNA TER cards. I have probably experienced > difficulties with them before, so that may solve one of the problems, but > not, I think, the other. > > Here are two pdb files from the pymol session. Ecoli_HSS_rot.pdb is the > target structure; Stau_urz_rot.pdb is the result output for the input > Stau_urz.pdb file. As you can see, even though the residues are, as far as > I can tell correctly indicated, the rotated file is off by about 90 degrees. > > Many thanks for any help. > > Charlie > > > > On Sep 10, 2018, at 5:36 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk > <eleanor.dod...@york.ac.uk>> 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 <car...@med.unc.edu> 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
