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, <hbo...@pasteur.edu.uy> 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 <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 >>> >> >> >> -- >> Scanned by iCritical. >> >> > > -- Scanned by iCritical.
