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.
