Program : LIGCOM
Version : 070213
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 596,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : compare geometry of hetero entities
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt (2006). CCP4 Proceedings. Acta Cryst. Submitted.
* 2 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.
060502 - 0.3 - first documented version
061111 - 0.4 - changed a few defaults; count and calculate RMSD of
well-superimposed atoms (e.g., within 2.0 A); list
RMS differences of fixed, flexible and all dihedrals;
added "caveat emptor" paragraph to manual
070212 - 0.5 - skip all except the first MODEL (in case of NMR entries)
in both the input PDB files;
bail out if no atoms encountered in either PDB file;
for atoms with alternate conformations, only keep the
first one encountered (applied to both input PDB files);
list distances between atoms after superpositioning;
changed the output somewhat
070213 - 0.6 - increased max nr of atoms to 500;
more error checks to prevent crashes in ValLigURL
This program can be used to assess the quality of hetero entities in PDB files (or to compare the geometry of two experimental structures).
LIGCOM will read two PDB files, each containing coordinates for one particular type of hetero entity. The compound found in the first file is assumed to be 'ideal' and the one in the second file is compared to it (distances, bond angles, impropers and 0/180 degree dihedrals). The second molecule can also be superimposed onto the first and the transformed coordinates saved to a new file.
Normally, the program will be run without arguments, and the user will be prompted for file names as well as the values of the various cut-offs to use. If the default values are okay, then the file names can also be provided on the command line, and no further input will be required, for instance:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- LIGCOM 869_ideal.pdb 1sqi_869_1501.pdb 1sqi_869_1501_super.pdb ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Please use this program sensibly and realise its limitations ! In particular, it does not do any atom-typing so it doesn't know which bonds are single or double, or even if two atoms are of the same type. As a consequence, it uses a hard-wired cut-off distance to decide if two atoms are bonded which will only work well for organic molecules without esoteric elements. Also, when an improper is listed as deviating a lot this doesn't mean there's necessarily anything wrong. For instance, if you inter-change the labels of two phosphate oxygen atoms you will get large deviations in the respective impropers but since the atoms are equivalent this is no reason for concern. Further, the program doesn't know which dihedrals ought to be fixed at values close to 0 or 180 degrees - it just sees if they happen to be close to either of these values. However, a value of 180 degrees may also occur for perfectly staggered 1-4 interactions and hence the value of such dihedrals in the other compound may well be close to +60 or -60 leading to seemingly large deviations. In actual fact, the dihedral is conformational and not fixed.
In other words: please check the output critically and apply your chemical knowledge !
Example of a batch run with default parameters:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- unix > LIGCOM myr_msd.pdb 1hbk_myr.pdb 1hbk_myr_super.pdb*** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM ***
Version - 060502/0.3 (c) 1992-2005 Gerard J. Kleywegt, Dept. Cell Mol. Biol., Uppsala (SE) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
Started - Tue May 2 20:23:09 2006 User - gerard Mode - interactive Host - sarek (Irix/SGI) ProcID - 13769 Tty - /dev/ttyq15
*** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM ***
Reference(s) for this program:
* 1 * G.J. Kleywegt (1992-2005). Uppsala University, Uppsala, Sweden. Unpublished program.
* 2 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.
==> For manuals and up-to-date references, visit: ==> http://xray.bmc.uu.se/usf ==> For reprints, visit: ==> http://xray.bmc.uu.se/gerard ==> For downloading up-to-date versions, visit: ==> ftp://xray.bmc.uu.se/pub/gerard
*** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM ***
Cut-off for bonded distances ........... : ( 2.000) Cut-off for printing distance deviations : ( 0.100) Cut-off for printing angle deviations .. : ( 10.000) Cut-off for printing improper deviations : ( 10.000) Cut-off for 0/180 degree dihedrals ..... : ( 10.000) Cut-off for printing dihedral deviations : ( 10.000)
PDB file with idealised ligand .. : (myr_msd.pdb) PDB file with experimental ligand : (1hbk_myr.pdb) Output superimposed PDB file .... : (1hbk_myr_super.pdb)
Nr of atoms in PDB file 1 : ( 16) Residue code : (MYR) Residue id : (MYR 4309) Residue id : (MYR A1090) Nr of atoms recognised : ( 12) File 1 atom not found : ( O1) File 1 atom not found : ( O2) File 1 atom not found : ( C13) File 1 atom not found : ( C14) RMSD common atoms (A) : ( 1.987) RT operator : ( -0.969 -0.240 -0.051 -0.241 0.971 -0.002 0.050 0.010 -0.999 -1.626 -17.810 17.472)
Atom 1 Atom 2 Dist 1 Dist 2 Diff ------ ------ ------ ------ ---- Nr of distances checked : ( 11) Nr of distances listed : ( 0) Nr of bonding distances : ( 11) RMS diff bond length (A): ( 0.015)
Atom 1 Atom 2 Atom 3 Ang 1 Ang 2 Diff ------ ------ ------ ----- ----- ---- Nr of angles checked : ( 10) Nr of angles listed : ( 0) RMS diff bond angles : ( 2.236)
Atom 1 Atom 2 Atom 3 Atom 4 Imp 1 Imp 2 Diff ------ ------ ------ ------ ----- ----- ---- Nr of impropers checked : ( 0) Nr of impropers listed : ( 0)
Atom 1 Atom 2 Atom 3 Atom 4 Dih 1 Dih 2 Diff ------ ------ ------ ------ ----- ----- ---- C1 - C2 - C3 - C4 180.0 -73.4 106.6 C2 - C3 - C4 - C5 -180.0 -74.8 105.2 C3 - C4 - C5 - C6 180.0 -150.0 30.0 C5 - C6 - C7 - C8 180.0 68.8 -111.2 C6 - C7 - C8 - C9 -180.0 66.4 -113.6 C7 - C8 - C9 - C10 180.0 -166.6 13.4 C8 - C9 - C10 - C11 -180.0 -67.3 112.7 Nr of dihedrals checked : ( 9) Nr of dihedrals listed : ( 7) RMS diff dihedrals : ( 82.648)
*** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM ***
Version - 060502/0.3 Started - Tue May 2 20:23:09 2006 Stopped - Tue May 2 20:23:09 2006
CPU-time taken : User - 0.0 Sys - 0.0 Total - 0.1
*** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM ***
>>>>>>>>>>>>>> USF .... Uppsala Software Factory <<<<<<<<<<<<<< >>>>>>>>>> This program: (c) 1992-2005, G J Kleywegt <<<<<<<<<< >>>>>>>>>>>>>>>> E-mail: gerard@xray.bmc.uu.se <<<<<<<<<<<<<<<< >>>>>>>>>>>>>>>>>> http://xray.bmc.uu.se/usf <<<<<<<<<<<<<<<<<<
*** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM *** LIGCOM ***
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example of an interactive run in which the parameters can be given values that differ from their defaults:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- unix > LIGCOM[...]
PDB file with idealised ligand .. ? (exper.pdb) myr_msd.pdb PDB file with experimental ligand ? (ideal.pdb) 1hbk_myr.pdb Output superimposed PDB file .... ? ( ) 1hbk_myr_super.pdb
Cut-off for bonded distances ........... ? ( 2.000) 1.8 Cut-off for printing distance deviations ? ( 0.100) 0.05 Cut-off for printing angle deviations .. ? ( 10.000) 5 Cut-off for printing improper deviations ? ( 10.000) 5 Cut-off for 0/180 degree dihedrals ..... ? ( 10.000) 5 Cut-off for printing dihedral deviations ? ( 10.000) 5
Cut-off for bonded distances ........... : ( 1.800) Cut-off for printing distance deviations : ( 0.050) Cut-off for printing angle deviations .. : ( 5.000) Cut-off for printing improper deviations : ( 5.000) Cut-off for 0/180 degree dihedrals ..... : ( 5.000) Cut-off for printing dihedral deviations : ( 5.000)
[...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The following example shows how you could use the program in practice.
(1) Get ideal coordinates for your compound (e.g., from MSDChem, AFITT, PRODRG, HIC-Up, etc.)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- curl -v http://xray.bmc.uu.se/hicup/REA/rea_msd.pdb > rea_msd.pdb ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
(2) Get experimental coordinates from your (own) structure
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- grep -i rea 1cbs.pdb > 1cbs_rea.pdb ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
(3) Run LIGCOM and check the printed output for missing atoms and unexpectedly large deviations from ideal geometry
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- LIGCOM rea_msd.pdb 1cbs_rea.pdb 1cbs_rea_super.pdb ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
(4) Load the ideal and the experimental coordinates into your favourite molecular graphics program to inspect them
None, at present ("peppar, peppar").
Does not compute.
Created at Tue Feb 13 15:05:04 2007
by MAN2HTML version 070111/2.0.8 . This manual
describes LIGCOM, a program of the Uppsala
Software Factory (USF), written and maintained by Gerard Kleywegt. © 1992-2007.