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 <[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]
>> <[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.
>>
>>
>>
>>
>>
>>
>
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