Program : AVEPDB
Version : 960415
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : average molecular structures using Cartesian or internal
coordinates
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt (1992-1999). Uppsala University, Uppsala, Sweden. Unpublished program.
* 2 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
Compute an average structure from the coordinates of several identical copies of a molecule, for example those related by non-crystallographical symmetry.
You may either average PDB files or BAD files (created with MOLEMAN; see the MOLEMAN manual for mor info); the latter is recommended for structures which are considerably different.
you have to supply the number of files
and their names, as well as a symmetry opeartor for EACH
file.
Note that the atoms must have the same names, atom numbers
etc. in all files (use MOLEMAN if this is not yet the case) !
Note that temperature factors and occupancies are also
averaged !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----*** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB ***
Version - 930214/0.5 By - Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL)
Started - Sun Feb 14 21:11:53 1993 User - gerard Mode - interactive Tty - /dev/ttyq1
*** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB ***
Max number of input files : ( 50)
Average PDB or BAD files (P/B) ? (P) p How many PDB files (2-99) ? ( 3) 2 Name of file nr 1 ? (junk.pdb) m3a.pdb Symm oper ? ( 1.000E+00 0.000E+00 0.000E+00 0.000E+00 1.000E+00 0.000E+00 0.000E+00 0.000E+00 1.000E+00 0.00 0.2797650 -0.9576010 0.0687860 -0.8472310 -0.2799500 -0.4514730 0.4515880 0.0680290 -0.8896290 33.893 Name of file nr 2 ? (m3a.pdb) m3b.pdb Symm oper ? ( 1.000E+00 0.000E+00 0.000E+00 0.000E+00 1.000E+00 0.000E+00 0.000E+00 0.000E+00 1.000E+00 0.00
Output (average) PDB file ? (average.pdb) m3ave.pdb
Nr of atoms averaged : 1099 Nr in main-chain : 500 RMS distance ALL ATOMS = 1.200431 RMS distance MAIN CHAIN = 0.9593915
*** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB ***
Version - 930214/0.5 Started - Sun Feb 14 21:11:53 1993 Stopped - Sun Feb 14 21:12:27 1993
CPU-time taken : User - 1.5 Sys - 0.2 Total - 1.7
*** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB ***
STOP ... All done ... statement executed ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- < % 236 gerard rigel 21:00:56 progs/avepdb> head m3a.pdb m3b.pdb m3ave.pdb ==> m3a.pdb <== REMARK FILENAME="m3a.pdb" REMARK PDB file created by MOLEMAN version 930205/2.6 at Fri Feb 5 22:17:19 1993 REMARK MoleMan PDB file REMARK DATE:12-Feb-93 14:01:33 created by user: gerard ATOM 1 CB PRO 2 3.860 27.223 -12.947 1.00 20.00 AAA1 ATOM 2 CG PRO 2 3.165 26.246 -13.837 1.00 20.00 AAA1 ATOM 3 C PRO 2 5.651 28.742 -13.736 1.00 20.00 AAA1 ATOM 4 O PRO 2 6.479 27.910 -14.137 1.00 20.00 AAA1 ATOM 5 HT1 PRO 2 3.287 28.951 -15.673 1.00 0.00 AAA1 ATOM 6 HT2 PRO 2 4.327 27.587 -15.734 1.00 0.00 AAA1==> m3b.pdb <== REMARK PDB file created by MOLEMAN version 930214/3.2 at Sun Feb 14 21:04:01 1993 REMARK MoleMan PDB file REMARK FILENAME="m3b.pdb" REMARK PDB file created by MOLEMAN version 930205/2.6 at Fri Feb 5 22:17:19 1993 REMARK MoleMan PDB file REMARK DATE:12-Feb-93 14:01:34 created by user: gerard ATOM 1 CB PRO 2 4.484 6.667 127.718 1.00 20.00 BBB1 ATOM 2 CG PRO 2 5.661 6.912 128.669 1.00 20.00 BBB1 ATOM 3 C PRO 2 3.240 4.410 127.666 1.00 20.00 BBB1 ATOM 4 O PRO 2 2.695 3.489 128.288 1.00 20.00 BBB1
==> m3ave.pdb <== ATOM 1 CB PRO 2 5.273 7.414 126.739 1.00 20.00 AAA1 ATOM 2 CG PRO 2 5.978 7.976 127.807 1.00 20.00 AAA1 ATOM 3 C PRO 2 4.080 5.189 126.782 1.00 20.00 AAA1 ATOM 4 O PRO 2 4.186 4.434 127.488 1.00 20.00 AAA1 ATOM 5 HT1 PRO 2 3.385 6.580 128.905 1.00 0.00 AAA1 ATOM 6 HT2 PRO 2 4.731 5.959 128.809 1.00 0.00 AAA1 ATOM 7 N PRO 2 4.244 6.667 128.508 1.00 20.00 AAA1 ATOM 8 CD PRO 2 4.982 7.882 128.690 1.00 20.00 AAA1 ATOM 9 CA PRO 2 4.142 6.594 127.233 1.00 20.00 AAA1 ATOM 10 N ALA 3 3.909 4.883 125.597 1.00 20.00 AAA1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
BAD files contain internal coordinates (generate with MOLEMAN):
read the relevant parts of the MOLEMAN manual FIRST (options EXPO,
SAME and IMPO) !
Do NOT use this option for disconnected fragments or chains;
run each of the fragments separately !!!
Note that the dihedrals are averaged by averaging their cosines
and their sines separately, and the average angle is computed
from the ATAN(sin_ave/cos_ave) !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----*** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB ***
Version - 930214/0.5 By - Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL)
Started - Sun Feb 14 21:19:53 1993 User - gerard Mode - interactive Tty - /dev/ttyq1
*** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB ***
Max number of input files : ( 50)
Average PDB or BAD files (P/B) ? (P) b How many BAD files (2-99) ? ( 3) 2 Name of file nr 1 ? (junk.pdb) m3a.bad Name of file nr 2 ? (m3a.bad) m3b.bad Output (average) BAD file ? (average.bad) m3ave.bad
Nr of atoms averaged : 1099 RMSD distances = 8.0489449E-02 RMSD angles = 3.912222 RMSD cosines = 0.3223881 RMSD sines = 0.3494238 RMSD occupancies = 0.0000000E+00 RMSD tem factors = 0.0000000E+00
*** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB ***
Version - 930214/0.5 Started - Sun Feb 14 21:19:53 1993 Stopped - Sun Feb 14 21:20:06 1993
CPU-time taken : User - 1.4 Sys - 0.2 Total - 1.6
*** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB *** AVEPDB ***
STOP ... All done ... statement executed ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- < % 249 gerard rigel 21:00:56 progs/avepdb> head m3a.bad m3b.bad m3ave.bad ==> m3a.bad <== BAD 1 N PRO 2 0.000 0.000 0.000 1.00 20.00 0 0 0 BAD 2 CA PRO 2 1.483 0.000 0.000 1.00 20.00 1 0 0 BAD 3 C PRO 2 1.544 116.750 0.000 1.00 20.00 2 1 0 BAD 4 O PRO 2 1.240 118.965 -58.380 1.00 20.00 3 2 1 BAD 5 CB PRO 2 2.477 34.960-122.016 1.00 20.00 3 2 1 BAD 6 CG PRO 2 1.493 123.219 67.598 1.00 20.00 5 3 2 BAD 7 CD PRO 2 1.522 100.087 -61.115 1.00 20.00 6 5 3 BAD 8 HT1 PRO 2 2.073 130.444 37.363 1.00 0.00 7 6 5 BAD 9 HT2 PRO 2 2.027 93.021 73.293 1.00 0.00 7 6 5 BAD 10 N ALA 3 1.359 115.762 125.518 1.00 20.00 3 2 1==> m3b.bad <== BAD 1 N PRO 2 0.000 0.000 0.000 1.00 20.00 0 0 0 BAD 2 CA PRO 2 1.479 0.000 0.000 1.00 20.00 1 0 0 BAD 3 C PRO 2 1.527 108.358 0.000 1.00 20.00 2 1 0 BAD 4 O PRO 2 1.238 117.202 50.223 1.00 20.00 3 2 1 BAD 5 CB PRO 2 2.578 32.836-116.704 1.00 20.00 3 2 1 BAD 6 CG PRO 2 1.533 121.535 69.951 1.00 20.00 5 3 2 BAD 7 CD PRO 2 1.516 102.795 -50.341 1.00 20.00 6 5 3 BAD 8 HT1 PRO 2 2.096 129.866 24.404 1.00 0.00 7 6 5 BAD 9 HT2 PRO 2 2.053 96.661 63.538 1.00 0.00 7 6 5 BAD 10 N ALA 3 1.358 117.896-132.394 1.00 20.00 3 2 1
==> m3ave.bad <== BAD 1 N PRO 2 0.000 0.000 0.000 1.00 20.00 0 0 0 BAD 2 CA PRO 2 1.481 0.000 0.000 1.00 20.00 1 0 0 BAD 3 C PRO 2 1.536 112.554 0.000 1.00 20.00 2 1 0 BAD 4 O PRO 2 1.239 118.083 -4.079 1.00 20.00 3 2 1 BAD 5 CB PRO 2 2.528 33.898-119.360 1.00 20.00 3 2 1 BAD 6 CG PRO 2 1.513 122.377 68.774 1.00 20.00 5 3 2 BAD 7 CD PRO 2 1.519 101.441 -55.728 1.00 20.00 6 5 3 BAD 8 HT1 PRO 2 2.084 130.155 30.883 1.00 0.00 7 6 5 BAD 9 HT2 PRO 2 2.040 94.841 68.415 1.00 0.00 7 6 5 BAD 10 N ALA 3 1.359 116.829 176.562 1.00 20.00 3 2 1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present.
Created at Fri Dec 18 19:42:06 1998
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