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 <[email protected]>
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 <[email protected]> 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 <[email protected]
>> <[email protected]>> 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 <[email protected]> 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
#CCP4I VERSION CCP4Interface 7.0.063
#CCP4I SCRIPT LOG superpose
#CCP4I DATE 10 Sep 2018 13:06:30
#CCP4I USER ed1
#CCP4I PROJECT shiftField
#CCP4I JOB_ID 15
#CCP4I SCRATCH /tmp/ed1
#CCP4I HOSTNAME kanga.chem.york.ac.uk
#CCP4I PID 2910
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
###############################################################
###############################################################
###############################################################
### CCP4 7.0.063: LSQKAB version 7.0.063 : ##
###############################################################
User: ed1 Run date: 10/ 9/2018 Run time: 13:06:30
Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
as well as any specific reference in the program write-up.
<!--SUMMARY_END--></FONT></B>
Data line--- title [No title given]
Data line--- fit res CA 11 to 100 chain A
Data line--- match 8 to 97 chain A
Data line--- fit res CA 101 to 130 chain A
Data line--- match 100 to 129 chain A
Data line--- output xyz
Data line--- end
LSQKAB RUN
[No title given]
OPEN FILES AS REQUESTED
Opening coordinate file of model to be moved
Logical name: XYZIN2 File name: /y/people/ccp4/Downloads/Ecoli_HSS_rot.pdb
PDB file is being opened on unit 1 for INPUT.
$WARNING: NO CRYST CARDS READ$
$WARNING: NO SCALE CARDS READ$
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
$TEXT:Warning: $$ comment $$
WARNING: No Space group given on PDB CRYST1 line
$$
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
$TEXT:Warning: $$ comment $$
WARNING: NO CRYST CARDS READ FROM XYZIN2
$$
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
$TEXT:Warning: $$ comment $$
WARNING: NO SCALE CARDS READ FROM XYZIN2
$$
<!--SUMMARY_END--></FONT></B>
Logical name: XYZOUT File name: /y/people/ccp4/projects/shiftField/Ecoli_HSS_rot_lsq1.pdb
PDB file is being opened on unit 2 for OUTPUT.
Opening coordinate file of fixed model.
Logical name: XYZIN1 File name: /y/people/ccp4/Downloads/Stau__urz_rot.pdb
PDB file is being opened on unit 3 for INPUT.
$WARNING: NO CRYST CARDS READ$
$WARNING: NO SCALE CARDS READ$
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
$TEXT:Warning: $$ comment $$
WARNING: No Space group given on PDB CRYST1 line
$$
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
$TEXT:Warning: $$ comment $$
WARNING: NO CRYST CARDS READ FROM XYZIN1
$$
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
$TEXT:Warning: $$ comment $$
WARNING: NO SCALE CARDS READ FROM XYZIN1
$$
<!--SUMMARY_END--></FONT></B>
- NO MATCH FOR WORKCD ATOM - 55CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 56CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 57CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 58CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 59CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 60CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 61CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 62CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 63CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 64CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 65CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 115CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 116CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 117CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 118CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 119CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 120CA A IN REFRCD FILE
- NO MATCH FOR WORKCD ATOM - 121CA A IN REFRCD FILE
** ZERO OCCUPANCIES IN WORKING SET ** 0.0
** ZERO OCCUPANCIES IN REFERENCE SET ** 0.0
LSFIT
2936 ATOMS IN WORKING MOLECULE( 102 TO BE REFINED)
885 ATOMS IN REFERENCE MOLECULE
CENTROID OF "WORKING" MOLECULE : 4.894 61.358 164.000
CENTROID OF "WORKING" MOLECULE :(fractional) 4.894 61.358 164.000
CENTROID OF "REFERENCE" MOLECULE: 9.935 64.979 157.959
CENTROID OF "REFERENCE" MOLECULE:(fractional) 9.935 64.979 157.959
Distance between CENTROIDS : 8.661
Direction cosines of vector between CENTROIDS: -0.582 -0.418 0.697
NUMBER OF ATOMS EXCLUDED BY RADCHK IS 0
RMS B DISPLACEMENT = 32.798
AVERAGE B DISPLACEMENT = 29.791
RMS XYZ DISPLACEMENT = 1.265
AVERAGE XYZ DISPLACEMENT = 0.938
MAXIMUM XYZ DISPLACEMENT = 6.190
ROTATION MATRIX:
0.51777 0.68956 0.50637
-0.71433 0.02274 0.69944
0.47079 -0.72387 0.50435
TRANSLATION VECTOR IN AS -117.95400 -47.62902 117.35677
TRANSLATION VECTOR IN fractions of cell edge -117.954002 -47.629021 117.356766
ROTATION MATRIX
0.518 0.690 0.506
-0.714 0.023 0.699
0.471 -0.724 0.504
PATTERSON SPHERICAL POLARS OMEGA PHI CHI OMEGA TO AXIS ZO PHI FROM AXIS XO TO AXIS YO
WHEN BETA=0 CAN ONLY DEFINE ALPHA + GAMMA .
WHEN BETA = 180 CAN ONLY DEFINE GAMMA - ALPHA.
trace 1.0448653
not 10- dc(1),dc(2),dc(3),chk -0.71183383 1.77939907E-02 -0.70212245 1.0000000
CROWTHER (Euler) ALPHA BETA GAMMA 54.09675 59.71184 -123.03950
SPHERICAL POLARS OMEGA PHI CHI 134.59764 178.56821 88.71467
DIRECTION COSINES OF ROTATION AXIS -0.71183 0.01779 -0.70212
Angle between rotation axis and Centroid vector 94.75086
***** Note: Since this angle between rotation axis and Centroid vector is near to 90.0 this may represent a pure rotation ***
THE TRANSLATION VECTOR IN ANGSTROMS ALONG THE ORTHONORMAL AXES IS
-117.95400 -47.62902 117.35677
THE TRANSLATION VECTOR IN FRACTIONS of the CELL EDGE IS
-117.954002 -47.629021 117.356766
2936 ATOMS WRITTEN TO "LSQOP"
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
LSQKAB: Normal Termination
Times: User: 0.0s System: 0.0s Elapsed: 0:00
</pre>
</html>
<!--SUMMARY_END--></FONT></B>
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 10 Sep 2018 13:06:31
#CCP4I MESSAGE Task completed successfully
