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
signature.asc
Description: OpenPGP digital signature
