On Sep 10, 2018, at 8:12 AM, Eleanor Dodson <[log in to unmask]> 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
<15_superpose.log>
On 10 September 2018 at 12:53, Eleanor Dodson <[log in to unmask]> 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 <[log in to unmask]> 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 <[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-lsqkabFIT RESIDUE MAIN 8 TO 82MATCH 10 to 84FIT RESIDUE MAIN 83 TO 111MATCH 85 to 113FIT RESIDUE MAIN 122 TO 129MATCH 124 to 131OUTPUT XYZENDEND-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