My guess is that only atom pairs that are superposed to some measure of distance between them, are output. Can't say that I checked lsqkab code this weekend, but documentation does not suggest anything like that.
Is this a problem for you? note that you can use other aligners/superposers in CCP4, ssm or Gesamt which will output all coordinates.
Eugene
On 10 May 2014, at 21:00, <[log in to unmask]>
wrote:
> 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 <[log in to unmask]>:
>
>> 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
>>>
>>
>>
>> --
>> Scanned by iCritical.
>>
>>
>
>
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