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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