Hi Eugene, thanks for your response.
Yes, the program is LSQKAB. No aligment is pursued, the aim is just to
superpose models and get all the information as tables. Looking at old
jobs (CCP4 6.2: LSQKAB version 6.2 : 13/03/09), it seems it always did
the same, the results on xyz and B rms just a subset of the atoms
(most) being superposed are written to the log file. This is
independent on the specific PDB files in use (I have tested a few
only)....can this be confirmed by you/circumvented by the user (i.e.
by changing the com file) or eventualy solved?
Thanks again!
H
Quoting Eugene Krissinel <eugene.krissi...@stfc.ac.uk>:
I would say the guess is a wrong one. SS superposition is used only
as a seed for further refinement. SSM (superpose) outputs all
residues (not all atoms) and marks those which get aligned. Then,
superposition is done using aligned residues. Alignment !=
superposition.
As to LSQKAB, it's pure superposition, not alignment AFAIK.
Alignment should be given to LSQKAB in form of atom pairs that
should be used for superposition.
No idea what is wrong in this example though.
Eugene
On 9 May 2014, at 23:33, Tim Gruene wrote:
Dear H,
you are referring to superpose, but your logfile lists the output from
LSQKAB, which are two different programs. According to the man-page of
superpose, it uses secondary structure elements for superposition, so
maybe the missing atoms are those not part of a helix and not part of a
strand. Just a guess.
Best,
Tim
On 05/09/2014 08:05 PM, Horacio Botti wrote:
Dear all,
Why does (if it is suppossed to do so) Superpose output results for a
subset of atoms only? See a summary of log file below (just the top
lines, data on atoms, and final data and message). In the example,
results for residues 69-76 are absent, other atoms are absent as well,
but the number of atoms that were skipped in the analysis is 0 (NUMBER
OF ATOMS EXCLUDED BY RADCHK IS 0). Of course, the atoms for these
residues are present in the pdb files and no alternative conformations
are being modeled. If you display a table from the log graph window, you
find xyz RMS for all atoms including the missed atoms. I also need info
on B RMS, which are not displayed in log graph.
What can I do to get a complete log file?
Thanks in advance!
H
#CCP4I VERSION CCP4Interface 2.2.0
#CCP4I SCRIPT LOG superpose
#CCP4I DATE 09 May 2014 09:21:04
#CCP4I USER hbotti
#CCP4I PROJECT ......
#CCP4I JOB_ID 30
#CCP4I SCRATCH /tmp/hbotti
#CCP4I HOSTNAME pxf8.ipmont.lan
#CCP4I PID 8268
###############################################################
###############################################################
###############################################################
### CCP4 6.3: LSQKAB version 6.3 : 13/03/09##
###############################################################
User: hbotti Run date: 9/ 5/2014 Run time: 09:21:04
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst.
D50, 760-763.
as well as any specific reference in the program write-up.
Data line--- title ......................
Data line--- fit res MAIN 66 to 544 chain B
Data line--- match 66 to 544 chain C
Data line--- output xyz rms deltas
Data line--- end
LSQKAB RUN
..................
OPEN FILES AS REQUESTED
Opening coordinate file of model to be moved
Logical name: XYZIN2 File name: ...............
PDB file is being opened on unit 1 for INPUT.
MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
RF RO
0.010 -0.000 0.002 0.000 96.790 0.000 -19.210 -0.000
-0.000 0.008 -0.000 -0.000 0.000 133.030 0.000 0.000
0.000 -0.000 0.009 -0.000 0.000 0.000 106.024 -0.000
-0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000
Logical name: XYZOUT File name: ..................
Opening coordinate file of fixed model.
Logical name: XYZIN1 File name: ...........................
PDB file is being opened on unit 3 for INPUT.
MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
RF RO
0.010 -0.000 0.002 0.000 96.610 0.000 -18.928 -0.000
-0.000 0.008 -0.000 -0.000 0.000 132.960 0.000 0.000
0.000 -0.000 0.009 -0.000 0.000 0.000 106.156 -0.000
-0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000
FORMATTED UNKNOWN file opened on unit 7
Logical name: RMSTAB, Filename: .....................
FORMATTED UNKNOWN file opened on unit 8
Logical name: DELTAS, Filename: ......................
- NO MATCH FOR WORKCD ATOM - 142CA B IN REFRCD FILE
** ZERO OCCUPANCIES IN WORKING SET ** 0.0
** ZERO OCCUPANCIES IN REFERENCE SET ** 0.0
LSFIT
**** ATOMS IN WORKING MOLECULE(1915 TO BE REFINED)
**** ATOMS IN REFERENCE MOLECULE
CENTROID OF "WORKING" MOLECULE : 10.597 -61.757 22.304
CENTROID OF "WORKING" MOLECULE :(fractional) 0.151 -0.464 0.210
CENTROID OF "REFERENCE" MOLECULE: 13.208 -36.008 70.253
CENTROID OF "REFERENCE" MOLECULE:(fractional) 0.266 -0.271 0.662
Distance between CENTROIDS : 54.488
Direction cosines of vector between CENTROIDS: -0.048 -0.473 -0.880
NUMBER OF ATOMS EXCLUDED BY RADCHK IS 0
RMS B DISPLACEMENT = 13.133
AVERAGE B DISPLACEMENT = -8.353
RMS XYZ DISPLACEMENT = 0.360
AVERAGE XYZ DISPLACEMENT = 0.245
MAXIMUM XYZ DISPLACEMENT = 4.237
ROTATION MATRIX:
-0.80795 -0.52390 0.26974
-0.52128 0.42202 -0.74173
0.27475 -0.73988 -0.61407
TRANSLATION VECTOR IN AS -16.59985 12.12253 35.34469
TRANSLATION VECTOR IN fractions of cell edge -0.106590
0.091174 0.332951
Natom2 ROTATED CDS ATOMId2 Natom1 AtomId1
Bdiff XYZDiff
3906 42.25 -30.59 71.01 N SER B 66 7814 N C
66 12.086 1.362
3907 43.27 -30.91 72.03 CA SER B 66 7815 CA C
66 9.649 2.287
3908 43.70 -29.70 72.95 C SER B 66 7816 C C
66 10.009 1.369
3909 44.77 -29.07 72.82 O SER B 66 7817 O C
66 7.790 1.385
3912 42.76 -29.40 73.86 N ARG B 67 7820 N C
67 11.744 1.043
3913 42.67 -28.40 74.93 CA ARG B 67 7821 CA C
67 12.507 0.564
3914 41.65 -29.05 75.90 C ARG B 67 7822 C C
67 11.896 0.390
3915 40.61 -29.55 75.45 O ARG B 67 7823 O C
67 12.607 0.716
3923 41.99 -29.05 77.21 N ALA B 68 7831 N C
68 9.604 0.386
3924 41.22 -29.64 78.32 CA ALA B 68 7832 CA C
68 9.077 0.481
3925 39.74 -29.71 78.08 C ALA B 68 7833 C C
68 2.969 0.385
3926 39.12 -28.69 77.82 O ALA B 68 7834 O C
68 4.235 0.500
3979 23.07 -37.77 88.38 C ALA B 76 7887 C C
76 14.096 0.138
3982 22.36 -37.31 89.41 N SER B 77 7890 N C
77 17.094 0.216
3983 21.48 -38.12 90.25 CA SER B 77 7891 CA C
77 19.000 0.303
3984 20.25 -38.54 89.50 C SER B 77 7892 C C
77 19.023 0.180
3985 19.66 -39.57 89.81 O SER B 77 7893 O C
77 21.129 0.226
3988 19.85 -37.72 88.54 N GLY B 78 7896 N C
78 16.028 0.157
3989 18.67 -37.92 87.71 CA GLY B 78 7897 CA C
78 15.794 0.120
3990 18.62 -39.17 86.87 C GLY B 78 7898 C C
78 14.368 0.161
3992 17.39 -39.61 86.58 N ASP B 79 7900 N
C 79
.
.
.
ROTATION MATRIX
-0.808 -0.524 0.270
-0.521 0.422 -0.742
0.275 -0.740 -0.614
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 -0.99999118
CROWTHER (Euler) ALPHA BETA GAMMA 109.98429 -127.88448 69.62775
SPHERICAL POLARS OMEGA PHI CHI 63.94224 -69.82162 179.82997
DIRECTION COSINES OF ROTATION AXIS 0.30988 -0.84322 0.43928
Angle between rotation axis and Centroid vector 90.16864
***** 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
-16.59985 12.12253 35.34469
THE TRANSLATION VECTOR IN FRACTIONS of the CELL EDGE IS
-0.106590 0.091174 0.332951
15722 ATOMS WRITTEN TO "LSQOP"
LSQKAB: Normal Termination
Times: User: 1.4s System: 0.0s Elapsed: 0:01
###############################################################
###############################################################
###############################################################
### CCP4 6.3: PDB_MERGE version 6.3 : ##
###############################################################
User: hbotti Run date: 9/ 5/2014 Run time: 09:21:05
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst.
D50, 760-763.
as well as any specific reference in the program write-up.
Data line--- nomerge
Data line--- end
PDB file ................... has been read in.
Read in 15773 atoms from XYZIN1
PDB file /tmp/hbotti/COMP-N-TcG6PDH_30_1_pdb.tmp has been read in.
Read in 15722 atoms from XYZIN2
XYZIN2 will be appended to XYZIN1 keeping constituent chains separate.
Checking for duplication of chain A ....
... replacing duplicated chain ID A by new_chain_id E
Checking for duplication of chain B ....
... replacing duplicated chain ID B by new_chain_id F
Checking for duplication of chain C ....
... replacing duplicated chain ID C by new_chain_id G
Checking for duplication of chain D ....
... replacing duplicated chain ID D by new_chain_id H
Some chains from XYZIN2 renamed.
........
Times: User: 0.2s System: 0.0s Elapsed: 0:00
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 09 May 2014 09:21:06
#CCP4I TERMINATION OUTPUT_FILES ........................
#CCP4I MESSAGE Task completed successfully
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
--
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