Eleanor, I’ve come up with a work-around for both problems. The problem with the tRNA file, I countered by using that pdb file as the fixed file, and so got round the need to write out a rotated pdb file (it still did not write out the output file, even though the rmsd was 0!).
The second problem, with the Stau coordinates, I got round by rotating them first into a new orientation. That suggests that there is a mathematical singular point for the rotation problem. I don’t know whether or not that can be fixed by some test on the singularity of the rotation matrix or something like that. Many thanks for your shoulders while I worked out of this rabbit hole! Charlie On Sep 10, 2018, at 8:12 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote: yes - I see that but when I run lsqkab on your two coordinate sets lsqkab works OK. Here is the command file - i made a guess on what to match.. ******************************************************************* /tmp/shiftField_15_1_com.tmp ******************************************************************* title [No title given] fit res CA 11 to 100 - chain A match 8 to 97 - chain A fit res CA 101 to 130 - chain A match 100 to 129 - chain A output - xyz end ## This script run with the command ########## # /y/programs/xtal/64bit/ccp4-7.0/2016-08-23-1/ccp4-7.0/bin/lsqkab XYZIN2 "/y/people/ccp4/Downloads/Ecoli_HSS_rot.pdb" XYZIN1 "/y/people/ccp4/Downloads/Stau__urz_rot.pdb" XYZOUT "/y/people/ccp4/projects/shiftField/Ecoli_HSS_rot_lsq1.pdb" ################################################ And I attach the log file. Indeed the Ecoli one is now rotated by ~ 90 degrees and fits quite well.. There is a lot of unmatched stuff of course for the Ecoli one but that shouldnt prevent the fit.. Eleanor On 10 September 2018 at 12:53, Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote: 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<mailto: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<mailto: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<mailto: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. <15_superpose.log> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
