Program : VOIDOO
Version : 981123
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 : cavity detection, volume calculation, surface generation
Package : VOIDOO
Reference(s) for this program:
* 1 * G.J. Kleywegt & T.A. Jones (1993). Biomacromolecular Speleology. CCP4/ESF-EACBM Newsletter on Protein Crystallography 29, November 1993, pp. 26-28. [http://alpha2.bmc.uu.se/usf/factory_2.html]
* 2 * G.J. Kleywegt & T.A. Jones (1994). Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Cryst D50, 178-185. [http://www.iucr.ac.uk/journals/acta/tocs/actad/1994/actad5002.html]
* 3 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
Version 0.1 @ 920807 - basic algorithm & documentation
Version 0.2 @ 920810 - altered definition of Vanderwaals radii
- sped up protein finder algorithm by factor 400
- atom fattening to detect "true" nr of cavities
- output proper mask file
- implemented volume refinement
- implemented simple ODL files
Version 0.3 @ 920811 - also read residue definitions from library file
- removed references to unit cell data (not used)
- add/subtract grid spacing to/from lower/upper limits
to account for the fact that we don't use the grid
points on the borders
- added probe radius
- implemented iterative zapping instead of recursive
(it's a bit faster and it doesn't crash with huge
grids)
- use character*1 parameters for filling the grid
- added volume option
- made MASK and ODL files optional
- implemented trace option to reduce output for normal
non-debugging runs
Version 0.4 @ 920812 - improved test file vol.pdb for volume testing
- took some Vanderwaals radii from the AMBER paper:
SJ Weiner et al., JACS 106, 765-784 (1984)
- implemented refinement for volume calculation option
- exclude borders in iterative zapping routines
- debugged grid-definition code (... aaarrgghhh ...)
- made it possible to actually perform all N detection
cycles (rather than only the "first best" option)
- made refinement optional
- implemented percentage convergence criterion
- removed several smaller bugs which only showed up in
"unfortunate" cases
Version 0.5 @ 920813 - implemented 1-sweep contour odl-output
- implemented 3-sweep contour odl-output
- updated documentation
Version 0.6 @ 920814 - implemented residue/atom combinations in vdw-lib
Version 0.7 @ 920820 - implemented dots odl-output
- added option to exclude probe from cavity volume
- print average/sigma of volumes calculated
Version 0.8 @ 920821 - use probe radius in volume calculation (if 1.4 Å =>
gives solvent-excluded volume)
- implemented option to look for a specific cavity by
providing XYZ-coordinates of a point you think or know
is inside it
- implemented output of ODL file which contains dots for
the protein surface points
Version 0.9 @ 920825 - implemented EZD plot output for cavities
Version 1.0 @ 920826 - implemented EZD plot output for protein itself
Version 1.1 @ 920922 - don't bail out if primary grid is too small and the
program is run interactively
- write cavity box to log file (for future option to
cut out a certain box to do the calculations on in
case you are looking for a specific cavity and want
to use a very fine primary grid)
- only allow error recovery in file open routines
(XOPxxx) if program is run interactively
Version 1.2 @ 920923 - implement limits on X,Y,Z to see if it works
Version 1.3 @ 921020 - problems with limit option -> removed it again
(couldn't always find "outside world")
Version 1.4 @ 921029 - altered find_spec_cavity so that the program
checks a 11*11*11 cube around the coordinates
that the user entered (used to be 5*5*5);
also changed so that closest point is selected;
doubled buffer size to 2 megawords
Version 1.5 @ 930202 - print radius of corresponding sphere whenever a
(cavity or molecular) volume is calculated;
doubled buffer size again, now to 4 megawords;
implemented new EZD format
Version 1.6 @ 930222 - minor changes
Version 2.0 @ 930302 - attempted to implement Connolly's "solvent-
occupied volume" ... it works !!!
Version 2.1 @ 930607 - implement molecule pre-rotation
Version 2.2 @ 930618 - print list of non-included atoms inside cavities
also print list of protein atoms lining it
Version 2.3 @ 930630 - removed bugs from these two new options
Version 2.4 @ 930809 - changed log-file format; new feature: IF plot
files are requested for the cavities, THEN also
O-macros to draw just the residues that are INSIDE
and those that are LINING the cavities are made
Version 2.4.1 930823 - include 'centre_xyz cavity_center_of_gravity'
in output O macros
Version 2.4.2 930825 - made NEWEZD format compatible with O 5.9.1
Version 3.0 @ 931116 - recognise HETATM cards; echo REMARK cards;
add comments to rotated PDB files; updated and
shortened this manual
Version 3.0.1 940715 - add "END" record to New-EZD maps
Version 3.1 @ 950118 - sensitive to environment variable GKLIB
960415 - 3.1.1 - minor bug fixes
971120 - 3.1.2 - changed "EZD" to "Old-EZD"; made (New-)EZD default
for output maps
981123 - 3.1.3 - minor bug fix (bail out if no atoms accepted)
VOIDOO is a program for computing molecular volumes and for
studying cavities in big molecules such as proteins. It
requires a PDB file, a library file and some additional input.
In order to do calculations with "randomly oriented" molecules,
an option to apply pseudo-random rotations to molecules in
PDB files is also supplied.
NOTE: This program is sensitive to the environment variable GKLIB. If set, the name of this directory will be prepended to the default name for the library file needed by this program. For example, in Uppsala, put the following line in your .login or .cshrc file: setenv GKLIB /nfs/public/lib
Supply a seed integer for the random number generator (identical seeds give identical rotations, so you can reproduce the results if you remember the seed !), an existing PDB file and a PDB file for the rotated molecule. This option is supported from version 2.1 and higher.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Select one of the following types of calculation: C = cavity calculations V = volume calculations R = rotate a moleculeType of calculation (C/V/R) ? (C) r 2 CPU total/user/sys : 0.1 0.0 0.1 => Random number generator initialised with seed : 3 Seed for random number generator ? ( 0) 1234567 => Random number generator initialised with seed : 1234567 Rotations around X,Y,Z (deg) : 180.19 207.54 160.97
X Matrix : 1.0000000 0.0000000 0.0000000 0.0000000 -0.9999947 0.0032597 0.0000000 -0.0032597 -0.9999947 Determinant of X rotation matrix : ( 1.000E+00) Y Matrix : -0.8866662 0.0000000 0.4624100 0.0000000 1.0000000 0.0000000 -0.4624100 0.0000000 -0.8866662 Determinant of Y rotation matrix : ( 1.000E+00) Z Matrix : -0.9453575 0.3260356 0.0000000 -0.3260356 -0.9453575 0.0000000 0.0000000 0.0000000 1.0000000 Determinant of Z rotation matrix : ( 1.000E+00) Matrix : 0.8382166 -0.2890848 0.4624100 0.3274588 0.9448611 -0.0028903 -0.4360777 0.1538429 0.8866615 Determinant of random rotation matrix : ( 1.000E+00)
Input PDB file name ? (in.pdb) m26.pdb
Output PDB file name ? (out.pdb) rot.pdb
Reading, rotating and writing ...
Number of lines read : ( 1240) Number of atoms read : ( 1236) ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that VOIDOO stores an account of how the rotated file was created through a number of REMARK records at the beginning of the new file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 920 gerard rigel 22:18:28 cavity/crbpm26 > head -10 rot.pdb REMARK Created by VOIDOO V. 931116/3.0 at Tue Nov 16 22:21:58 1993 for user gerard REMARK Created by rotating atoms in file m26.pdb REMARK Xnew = 0.8382166 * Xold + -0.2890848 * Yold + 0.4624100 * Zold REMARK Ynew = 0.3274588 * Xold + 0.9448611 * Yold + -0.0028903 * Zold REMARK Znew = -0.4360777 * Xold + 0.1538429 * Yold + 0.8866615 * Zold REMARK Seed 1234567 used for random number generator REMARK CRBP MODEL M26 (CELLULAR RETINOL-BINDING PROTEIN) ATOM 1 CB PRO 1 1.894 -9.180 -17.892 1.00 20.29 ATOM 2 CG PRO 1 2.453 -10.121 -18.947 1.00 20.79 ATOM 3 C PRO 1 1.321 -9.620 -15.461 1.00 18.52 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
We shall first discuss the volume-calculation option of the program, by going step-by-step through an example calculation, explaining all the input parameters.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 862 gerard rigel 21:07:29 cavity/crbpm26 > run voidoo... Run voidoo
... Executing /nfs/public/IRIX/bin/4d_voidoo ... For gerard on rigel at Tue Nov 16 21:11:15 MET 1993
*** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO ***
Version - 931116/3.0 (C) 1993 - Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) 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, etc. etc.
Started - Tue Nov 16 21:11:16 1993 User - gerard Mode - interactive Host - rigel ProcID - 8131 Tty - /dev/ttyq1
*** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO ***
***** VOIDOO ***** VOIDOO ***** VOIDOO ***** VOIDOO ***** VOIDOO *****
Current version : 930825/2.4.2 Max nr of atoms : 50000 Max nr of elements : 50 Max nr of atom types : 100 Max nr of residue/atom types : 500 Max nr of residue types : 50 Max nr of cavities : 500 Max nr of detection cycles : 50 Max nr of refinement cycles : 50 Max nr of grid points per axis : 500 Max nr of points for grid 1 : 4194304 Max nr of points for grid 2 : 4194304 Max nr of points for grid 3 : 250000 Memory use (Bytes) for major arrays : 9438608
***** VOIDOO ***** VOIDOO ***** VOIDOO ***** VOIDOO ***** VOIDOO *****
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Data input ----------Select one of the following types of calculation: C = cavity calculations V = volume calculations R = rotate a molecule
Type of calculation (C/V/R) ? (C) v ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
a flag which indicates whether you want to do volume or cavity calculations ('C' or 'V')
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Do you want extensive output ? (N) n ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
a flag which indicates whether or not you want extensive output (and I mean extensive ...); unless you have run into a bug or apparently strange results, you should reply 'N(o)' at this point
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----(1) Vanderwaals radii and residue types
Library file ? (cavity.lib) ../cavity.lib Reading your library file ... Nr of lines in library file : ( 132) Nr of elements defined : ( 14) Nr of atom types defined : ( 2) Nr of residue/atom types : ( 37) Nr of residue types defined : ( 21)
ELEM N 1.75 C 1.85 O 1.60 S 2.00 ... RESI THR TRP TYR VAL CPR ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
the name of an input library file; you may copy the example library (pertaining to proteins) and edit it at your heart's content. The library may/must contain the following key-worded information:
* comments, keyword 'REMA', followed by any text
* generic Vanderwaals radii for elements, keyword 'ELEM', followed by the element symbol (two characters !) and its radius
* specific Vanderwaals radii for certain atom types, keyword 'ATOM', followed by the atom name (four characters !) and its radius
* specific Vanderwaals radii for specific atoms in specific residues, keyword 'SPAT' followed by a string of the type 'RES*ATOM', where 'RES' is the residue name, '*' may be anything and 'ATOM' is the name of the atom, followed by its radius
* residue types which are to be read from the PDB file, keyword 'RESI', followed by the name of the residue type (three characters); if you want to measure the size of the cavity that your inhibitor is in, for example, you don't want to use the inhibitor's atoms to calculate the free volume, and therefore you don't read the inhibitor at all
* an end-of-file marker, keyword 'END '
Selected parts of such a file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMA cavity.lib - library of Vanderwaals radii and residue types REMA used by program VOIDOO REMA *** elements *** TWO characters; RIGHT justified REMA ELEM ' N' 1.75 ELEM ' C' 1.85 NOTE: all Cs are 1.85 in AMBER, except CH2/CH3 ELEM ' O' 1.60 (...) REMA *** atom types *** FOUR characters; element is first TWO REMA ATOM ' NZ ' 1.85 NOTE: occurs only in Lys (...) REMA *** residue/atom combinations *** EIGHT chracaters: RRR*AAAA REMA first three=residue, four=anything, five-eight=atom name REMA REMA OH = 1.65 REMA SPAT 'TYR* OH ' 1.65 SPAT 'THR* OG1' 1.65 REMA REMA CH2 = 1.925 REMA SPAT 'SER* CB ' 1.925 SPAT 'ASN* CB ' 1.925 (...) REMA CH3 = 2.00 REMA SPAT 'ALA* CB ' 2.00 SPAT 'THR* CG2' 2.00 SPAT 'LEU* CD1' 2.00 (...) REMA *** allowed residue types *** REMA RESI 'ALA' RESI 'ARG' RESI 'ASN' (...) RESI 'TYR' RESI 'VAL' RESI 'CPR' END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- (2) PDB filePDB file name ? (in.pdb) rot.pdb Reading your PDB file ... REMARK CREATED BY VOIDOO V. 931116/3.0 AT TUE NOV 16 22:21:58 1993 FOR USER GERARD REMARK CREATED BY ROTATING ATOMS IN FILE M26.PDB REMARK XNEW = 0.8382166 * XOLD + -0.2890848 * YOLD + 0.4624100 * ZOLD REMARK YNEW = 0.3274588 * XOLD + 0.9448611 * YOLD + -0.0028903 * ZOLD REMARK ZNEW = -0.4360777 * XOLD + 0.1538429 * YOLD + 0.8866615 * ZOLD REMARK SEED 1234567 USED FOR RANDOM NUMBER GENERATOR REMARK CRBP MODEL M26 (CELLULAR RETINOL-BINDING PROTEIN) Number of atoms read : ( 1236) Number of atoms kept : ( 1102) Number of atoms rejected : ( 134) Max Vanderwaals radius : ( 2.000) Sum of atomic volumes : ( 2.772E+04) Rejected residue types : ( RTL CD2 HOH) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
the name of your PDB file
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- (3) Primary gridMin, max, cog for X : -10.443 29.645 10.919 Min, max, cog for Y : -13.207 20.736 4.429 Min, max, cog for Z : -30.775 6.903 -10.179 Primary grid spacing (A) ? ( 1.000) 0.5 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
the spacing (in Angstrom) of the primary grid on which the initial steps (of detecting your molecule or cavities) will be performed. This value must be >= 0.01; if it is too small, the grid will not fit into the program's buffers and the program will bail out
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Probe radius (1.4 A for water) ? ( 0.000) 0 Min, max, cog for X : -12.500 32.000 Min, max, cog for Y : -15.500 23.000 Min, max, cog for Z : -33.000 9.000 Number of grid points : ( 90 78 85) Volume per voxel (A3) : ( 1.250E-01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
the probe radius is added to the Vanderwaals radii of the atoms; use 1.4 Å if you want to compute the solvent-excluded volume or 0.0 Å for the volume of the protein per se.
NOTE: the reason people often use 1.4 Å as the radius for a water molecule is based on the observation that the O-O distance in ice is ~2.8 Å. While this hardly justifies the use of a 1.4 Å radius for a solvent water, the fact that many have used this value and are still using it means that you can compare numbers slightly better than when you are using another (arbitrary) number (e.g., 1.2 Å or 1.8 Å).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- (4) Various parametersNr of volume-refinement cycles ? ( 10) 15 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
the number of volume-refinement cycles. Once your molecule has been detected on the primary grid, a number of refinement cycles can be carried out on increasingly fine grids, until the calculated volume converges. This number must lie between 1 and 1000
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Grid-shrink factor ? ( 0.900) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
the grid-shrink factor. This number determines how much finer the grid is made in each refinement cycle. The value must lie between 0.1 and 0.999; recommended are values of the order of 0.8 - 0.9
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Convergence criterion (A3) ? ( 0.100) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
an absolute volume-convergence criterion. If the difference in volume between two consecutive refinement cycles is less than this number, convergence has been achieved. This number must be >= 0.001
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Convergence criterion (%) ? ( 0.100) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
a relative volume-convergence criterion. If the percentage difference in volume between two consecutive refinement cycles is less than this number, convergence has been achieved. This number must lie between 0.001 and 99.999
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Create protein-surface plot file ? (N) y Dots, Old-EZD or New-EZD (D/O/N) ? (N) Name of this file ? (protein.ezd) Grid spacing to use ? ( 0.700) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
optionally, VOIDOO can be used to create files showing the surface of the protein when viewed with "O". You may produce either an ODL file (dots) or an EZD or NEWEZD file. ODL files can be viewed with the DRAW command in "O"; NEWEZD files can be displayed using the EZD_READ and EZD_DRAW options, or they can be converted into ordinary MAP files with MAPMAN. EZD files must first be converted with MAPMAN.
From version 3.1.2, (New-)EZD files are the default. They can be drawn directly using the FM_* commands in O. The Old-EZD format will be phased out, so don't use it.
The algorithm is rather simple:
* for each cycle do:
- initialise grid and calculate volume/voxel ratio
- label all grid points which lie within the Vanderwaals radius of an atom
- count all labelled points and multiply by the volume/voxel ratio
- if cycle > 1, compare with the volume found in the previous cycle and
test for convergence; if converged, jump out of the refinement loop
The algorithm's order is approximately linear with respect to the number of atoms, but inversely proportional to the third power of the grid spacing. For example, model M3 of gta requires 7.8 CPU seconds (on a slow Personal Iris) for a 1.0 Å grid and 10.7 seconds on a 0.9 Å grid; now 10.7 / 7.8 = 1.37 and 1/(0.9*0.9*0.9) = 1.37 !
The output during program execution may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- CYCLE : ( 1) Grid spacing : ( 0.500) Setting up grid ... Nr of points in grid : ( 596700) Not the protein : ( 481012) The protein itself : ( 115688) 23 CPU total/user/sys : 2.7 2.6 0.1 Nr of voxels in protein : ( 115688) Volume per voxel (A3) : ( 1.250E-01) Protein volume (A3) : ( 1.446E+04) Volume corresponds to a sphere of radius (A) : ( 1.511E+01) Nr of new grid points : ( 101 88 96)CYCLE : ( 2) Grid spacing : ( 0.450) Setting up grid ... Nr of points in grid : ( 853248) Not the protein : ( 694538) The protein itself : ( 158710) 23 CPU total/user/sys : 4.1 4.1 0.1 Nr of voxels in protein : ( 158710) Volume per voxel (A3) : ( 9.112E-02) Protein volume (A3) : ( 1.446E+04) Volume corresponds to a sphere of radius (A) : ( 1.511E+01)
>>> CONVERGENCE <<<
Last change (A3/%) : ( 1.447E+00 1.001E-02) Nr of volume calculations : ( 2) Average volume (A3) : ( 1.446E+04) Volume corresponds to a sphere of radius (A) : ( 1.511E+01) Standard deviation (A3) : ( 7.236E-01) 17 CPU total/user/sys : 0.9 0.9 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that the volume converges to within approximately 0.01 % in two cycles, but this could be accidental. In general, it's better to have a number of values so you can judge how sensitive the volume is to the chosen grid spacing. In this case, you could change the grid-shrink factor and/or the primary grid spacing and/or the convergence criteria.
Subsequently, VOIDOO will generate the protein-surface file and stop:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Protein plot grid : ( 92 80 87) Setting up grid ... Nr of points in grid : ( 640320) Not the protein : ( 524632) The protein itself : ( 115688) 23 CPU total/user/sys : 2.8 2.7 0.1 Nr of protein points : ( 115688) Nr of protein points : ( 115688) 32 CPU total/user/sys : 19.6 18.8 0.7*** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO ***
Version - 930825/2.4.2 Started - Tue Nov 16 21:11:16 1993 Stopped - Tue Nov 16 21:15:50 1993
CPU-time taken : User - 30.0 Sys - 1.1 Total - 31.1
*** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO ***
>>> This program is (C) 1993, GJ Kleywegt & TA Jones <<< E-mail: "gerard@xray.bmc.uu.se" or "alwyn@xray.bmc.uu.se"
*** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO ***
STOP ... Toodle pip ... statement executed
real 4:35.0 user 29.9 sys 1.1
... Started Tue Nov 16 21:11:15 MET 1993 ... Finished Tue Nov 16 21:15:51 MET 1993 ... Mode Normal
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
let's have a look at the surface plot file (note that a New-EZD file can be read into O directly !)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 865 gerard rigel 21:07:29 cavity/crbpm26 > head -10 crbp_surf.nezd EZD_MAP ! Created by VOIDOO V. 930825/2.4.2 at Tue Nov 16 21:15:32 1993 for user gerard CELL 100.000 100.000 100.000 90.000 90.000 90.000 ORIGIN -26 -32 -67 EXTENT 92 80 87 GRID 200 200 200 SCALE 1.000 MAP 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
We shall now deal with the cavity-related options of VOIDOO:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Select one of the following types of calculation: C = cavity calculations V = volume calculations R = rotate a moleculeType of calculation (C/V/R) ? (C) Do you want extensive output ? (N)
(1) Vanderwaals radii and residue types
Library file ? (cavity.lib) ../cavity.lib Reading your library file ... ... (2) PDB file
PDB file name ? (in.pdb) rot.pdb Reading your PDB file ... ... (3) Primary grid
Min, max, cog for X : -10.443 29.645 10.919 Min, max, cog for Y : -13.207 20.736 4.429 Min, max, cog for Z : -30.775 6.903 -10.179 Primary grid spacing (A) ? ( 1.000) 0.75 Probe radius (1.4 A for water) ? ( 1.400) 1.2 Min, max, cog for X : -14.250 33.000 Min, max, cog for Y : -16.500 24.000 Min, max, cog for Z : -34.500 10.500 Number of grid points : ( 64 55 61) Volume per voxel (A3) : ( 4.219E-01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The first few input items are the same as in the case of volume calculations.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Nr of detection cycles ? ( 10) 8 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
the maximum number of cavity-detection cycles
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Growth factor for Vanderwaals radii ? ( 1.100) 1.05 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
the growth factor for the Vanderwaals radii in the cavity-detection stage
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Min size of "real" cavities (voxels) ? ( 1) 5 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
minimum size (in voxels on the primary grid) of "real" cavities; this is to enable you to disregard (ridiculously) small cavities.
NOTE: Hubbard and Argos (Protein Engineering 8, 1011-1015) argue that, using a 1.2 Å probe radius a minimum volume of 10 Å**3 can be used for "real" cavities.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Are you looking for a specific cavity ? (N) n All cycles or First decline (A/F) ? (F) f ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
either look for a specific cavity (in which case you are prompted to supply the X, Y and Z coordinate of a "seed point" of which you know that it is inside the cavity (and not too close to any atoms, please) or detect unknown cavities by either finding the best growth factor after all cycles have been completed (A), or stop as soon as the number of cavities ceases to increase (F)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Do you want a MASK file ? (N) y MASK file name ? (out.mask) crbp.mask ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
create a MASK file or not; if you want one, supply its name
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- LOG file name ? (cavity.log) crbp_test.log ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
the name for your LOG file, to which a summary of the calculations and their results will be written
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Do you want to refine the cavities ? (Y) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
refine the cavities or not; if you only want to count the number of cavities, or to find the 'optimal' value for the growth factor, you should reply with 'N(o)' here
The algorithm for cavity detection is as follows:
* set the atom-fattening factor to 1.00
* for each cycle do
- initialise the grid
- flag all points on the grid which lie within a distance Dmin of an
atom, where
Dmin = (Vanderwaals radius) * (atom-fattening factor) + (probe radius)
- count the number of "real" (i.e., big enough) cavities
- cycle > 1 and option = 'F' then if the number of cavities is not higher
than that found in the previous cycle (unless there were zero then),
jump out of the loop
- multiply atom-fattening factor by Vanderwaals growth factor
* if option = 'A' then find the atom-fattening factor which gave the highest
number of cavities
* restore the grid using the best atom-fattening factor
* produce a MASK file if required
Again, the order of the algorithm is inversely proportional to the third power of the grid spacing.
The 'atom fattening' has been implemented in order to close cavities which are still connected to 'the outside world'. By artificially increasing the Vanderwaals radii, at a certain stage you will start to close those connections, which will be evidenced by an increasing number of detected cavities. When the atoms get too big, they will start to fill existing cavities and, hence, the number of cavities will decrease. If you make the atoms still bigger, the number of cavities will increase again, but these are not real cavities, but actually parts of thee outside world which have become isolated since the molecule 'expands' outside its 'box' (ie, the primary grid).
The probe radius also helps to close off connections to the outside world, but in addition it will ensure that you only find cavities which are big enough to contain a certain type of molecule/ion (eg, if you want to find possible water cavities, you may set the probe radius to 1.4 Å). The minimum cavity size (in voxels) may be used to the same effect.
The MASK file is created using the best atom-fattening factor and the probe radius. The mask will therefore give you an idea of the LOCATIONS of the cavities, but NOT of their EXTENT in space (since you have to correct for the fattened atoms and the probe radius; this is done in the refinement phase).
Output for the cavity-detection stage may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----Data input done ---------------
2 CPU total/user/sys : 1.3 1.0 0.2
DETECTION CYCLE : ( 1) Vanderwaals factor : ( 1.000) Setting up grid ... Nr of points in grid : ( 214720) Not the protein : ( 152956) The protein itself : ( 61764) Nr of non-protein points now : ( 132110) Nr of points outside protein : ( 131524) Nr of cavity points : ( 586) 23 CPU total/user/sys : 12.9 12.6 0.3 Cavity found ! Nr of points : ( 583) Nr of cavities found : ( 1) Total nr of points in cavities : ( 583) Total cavity volume : ( 2.460E+02) 8 CPU total/user/sys : 5.4 5.2 0.1 Nr of cavities : ( 1)
DETECTION CYCLE : ( 2) Vanderwaals factor : ( 1.050) Setting up grid ... Nr of points in grid : ( 214720) Not the protein : ( 151485) The protein itself : ( 63235) Nr of non-protein points now : ( 130640) Nr of points outside protein : ( 130143) Nr of cavity points : ( 497) 23 CPU total/user/sys : 12.9 12.7 0.2 Cavity found ! Nr of points : ( 493) Nr of cavities found : ( 1) Total nr of points in cavities : ( 493) Total cavity volume : ( 2.080E+02) 8 CPU total/user/sys : 5.3 5.0 0.3 Nr of cavities : ( 1) 4 CPU total/user/sys : 0.0 0.0 0.0 Setting up grid ... Nr of points in grid : ( 214720) Not the protein : ( 152956) The protein itself : ( 61764) Nr of non-protein points now : ( 132110) Nr of points outside protein : ( 131524) Nr of cavity points : ( 586) 23 CPU total/user/sys : 12.5 12.3 0.2 Writing mask 5 CPU total/user/sys : 5.4 5.2 0.2 6 CPU total/user/sys : 0.0 0.0 0.0 Vanderwaals factor employed : ( 1.000) Max Vanderwaals radius used : ( 2.000) Margin for adding to grid : ( 2.000)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
In this example, cycle 2 did not give more cavities than cycle 1,
so the detection stage finishes with one cavity found.
In case you want to refine the cavity volumes, the following additional input
is required:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Nr of volume-refinement cycles ? ( 10) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
the number of cavity-volume refinement cycles
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You may calculate one of these type of cavity volumes: (V) Vanderwaals: not occupied by the molecule (A) Probe-accessible: available to the probe centre (O) Probe-occupied: occupied by rolling probe Type of cavity volume (V/A/O) ? (A) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- Vanderwaals cavity: the complement of the molecule's Vanderwaals surface
(not recommended, unless the atoms without the probe close off the cavity)
- Probe-accessible: the volume accessible to the centre of the probe sphere
- Probe-occupied: the volume occupied by the probe; this gives nice "Connolly-
surfaces" of your cavity and the numerical results (provided that you use a
FINE grid for the cavities, less than approximately 0.25 Å) are comparable
to those obtained with Connolly's MS program. This type of cavity is
created from the probe-accessible cavity by adding all points which are
within the probe radius from the accessible cavity's surface to the cavity.
Use ONLY when your cavity is closed by the probe at the standard
Vanderwaals radii !!!
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Grid-shrink factor ? ( 0.900) 0.93 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- the grid-shrink factor
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Min size of secondary grid ? ( 10) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- the minimum size of the secondary grid (in any one dimension); this is to prevent calculations on a grid which is small and therefore relatively coarse (which makes the computed volume less reliable and usually leads to large variations in the volumes computed in consecutive cycles); use a large number if you want to compare your numerical results to those of Connolly's MS program
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Convergence criterion (A3) ? ( 0.100) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- an absolute convergence threshold (A3)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Convergence criterion (%) ? ( 0.100) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- a relative convergence threshold (%)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Create protein-surface plot file ? (N) no ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
protein-surface files; see under volume calculations
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Do you want plot files ? (Y) First part of plot file names ? (cavity) Grid for plot files ? ( 0.700) You may choose from the following types of graphical representations for your cavities: O * generate Old-EZD files N * generate New-EZD files D * draw dots for all cavity points 3 * 3-sweep contour (fairly quick) 1 * 1-sweep contour (quick and dirty) C * connect all surface points (fast/big objects) T * tiles (ie, poly-triangles; not implemented yet) Graphical representation (C/1/3/D/T/O/N)? (N) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
whether or not you want plot output files, which contain graphical
descriptions of the cavities and which can be drawn directly with "O";
if you want such files, then the following input is required as well:
- the first part of the plot file names (if you enter 'abc', then the
files for cavity 1, 2 etc will be called abc_1.o, abc_2.o etc.)
- the grid spacing to use for the graphical representations of cavities
(the finer you make this grid, the bigger the graphics objects will
become and the slower will drawing and manipulating them in "O" be);
use a fine grid (e.g., 0.2 Å) for plotting probe-occupied cavities !!!
- the type of graphical representation you want
HINT: use CPK models of your protein and/or ligand etc in conjunction
with the cavity drawings !
From version 3.1.2, (New-)EZD is the default.
The volume-refinement algorithm is as follows:
* for all cavities found in the primary grid do
- isolate the cavity
- for each refinement cycle do
o set up a secondary grid, compensating for the atom-fattening and the
probe radius used in the primary grid; each dimension must have at
least a certain number of grid points, if not multiply the grid size
by the grid-shrink factor and try again; if the grid no longer fits
the program's buffer, jump out of the loop
o initialise the secondary grid and compute the volume/voxel ratio
o label all points which are within the Vanderwaals radius of an atom
o isolate the cavity ("zapping")
o count the grid points that constitute the cavity and compute the
cavity's volume from that
o test for convergence
- afterwards, print the coordinates of the centre of cavity gravity etc.
- generate the plot files if required
* print the total number of cavities and their combined volume
Again, the order of the algorithm is inversely proportional to the third power of the grid spacing.
Output may look like this:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----NEW CAVITY ! Nr of points : ( 583) Zero-order volume : ( 2.460E+02) 9 CPU total/user/sys : 3.8 3.7 0.1
REFINEMENT CYCLE : ( 1) Grid spacing : ( 0.750) Nr of secondary grid points : ( 24 28 27) Volume per voxel (A3) : ( 4.219E-01) Setting up grid ... Nr of points in grid : ( 18144) Not the protein : ( 1426) The protein itself : ( 16718) 23 CPU total/user/sys : 0.8 0.7 0.0 Nr of points "zapped" : ( 583) 11 CPU total/user/sys : 0.2 0.2 0.0 Volume : ( 2.460E+02) Volume corresponds to a sphere of radius (A) : ( 3.887E+00)
...
REFINEMENT CYCLE : ( 10) Grid spacing : ( 0.390) Nr of secondary grid points : ( 43 51 49) Volume per voxel (A3) : ( 5.946E-02) Setting up grid ... Nr of points in grid : ( 107457) Not the protein : ( 7811) The protein itself : ( 99646) 23 CPU total/user/sys : 3.0 2.9 0.1 Nr of points "zapped" : ( 4142) 11 CPU total/user/sys : 3.1 3.0 0.0 Volume : ( 2.463E+02) Volume corresponds to a sphere of radius (A) : ( 3.888E+00) Centre of cavity gravity 12.371 9.891 -7.847 Nr of volume calculations : ( 10) Average volume (A3) : ( 2.462E+02) Volume corresponds to a sphere of radius (A) : ( 3.888E+00) Standard deviation (A3) : ( 1.385E+00) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Now VOIDOO will list the atoms that are inside this cavity, and those that line it:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Looking for atoms inside this cavity ... Inside > C1 RTL 200 @ 11.813 12.750 -5.950 Inside > C2 RTL 200 @ 11.812 13.896 -4.907 ... Inside > C15 RTL 200 @ 9.077 3.575 -11.205 Inside > O1 HOH 260 @ 16.834 7.214 -12.232 Nr found : ( 20)Looking for atoms lining this cavity ... Nr of candidates : ( 458) Lining > CE MET 10 @ 9.303 6.153 -1.218 Lining > ND2 ASN 13 @ 12.929 6.691 0.277 ... Lining > NE2 GLN 128 @ 12.436 5.329 -3.371 Lining > CZ PHE 130 @ 7.163 4.791 -3.985 Nr found : ( 106) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Finally, if you requested them, plot files and O macros will be generated:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Nr of plot grid points : ( 33 40 39) Setting up grid ... Nr of points in grid : ( 51480) Not the protein : ( 3707) The protein itself : ( 47773) 23 CPU total/user/sys : 64.1 63.1 1.0 Nr of points "zapped" : ( 1959) Nr of points "zapped" for plot : ( 1959) Volume per voxel (A3) : ( 1.250E-01) Cavity volume on plot grid (A3) : ( 2.449E+02) Volume corresponds to a sphere of radius (A) : ( 3.881E+00) 34 CPU total/user/sys : 2.8 2.7 0.1Summary : Nr of cavities found : ( 1) Nr of original grid points in cavities : ( 583) Total cavity volume : ( 2.463E+02)
*** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO ***
Version - 930825/2.4.2 Started - Tue Nov 16 21:19:55 1993 Stopped - Tue Nov 16 21:29:55 1993
CPU-time taken : User - 150.9 Sys - 3.5 Total - 154.5
*** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO ***
>>> This program is (C) 1993, GJ Kleywegt & TA Jones <<< E-mail: "gerard@xray.bmc.uu.se" or "alwyn@xray.bmc.uu.se"
*** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** VOIDOO *** ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The LOG file contains a summary of the input and the results:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 869 gerard rigel 21:07:29 cavity/crbpm26 > cat crbp_test.log ... - PDB file rot.pdb- MASK file crbp.mask
- LOG file crbp_test.log
- Plot files crbp_cav_#.o
- Grid & cavity parameters Max nr of cavity-detection cycles : 8 Will do detection cycles until first best Vanderwaals growth factor : 1.050 Probe radius : 1.200 Min nr of voxels in "real" cavities : 5 Max nr of volume-refinement cycles : 10 Will calculate probe-accessible volumes Will use probe in cavity-volume calculations Grid shrink factor : 0.930 Min size of secondary grid : 10 Grid for plot files : 0.500 Volume-convergence tolerance (A3) : 0.100 Volume-convergence tolerance (%) : 0.100 Primary grid spacing : 0.750 Grid sizes : 64 55 61 Lower X/Y/Z limits : -14.250 -16.500 -34.500 Upper X/Y/Z limits : 33.000 24.000 10.500 No plot file for protein surface will be made Plot grid spacing : 0.500 Representation: New-EZD
Determining number of cavities ... Cycle 1 | Vdw-factor 1.00000 | Cavities 1 ... Cycle 2 | Vdw-factor 1.05000 | Cavities 1 Best Vdw-factor 1.00000 gives 1 cavities
Refining cavity volumes
Cavity # 1 Starts at 8.250 3.750 -11.250 Cavity box 5.050 20.450 -0.200 18.950 -16.700 1.700 Cycle Grid V(vox) #Vox Cavity volume 1 0.75000 0.42188 583 2.45953E+02 2 0.69750 0.33934 722 2.45002E+02 3 0.64868 0.27295 906 2.47292E+02 4 0.60327 0.21955 1106 2.42821E+02 5 0.56104 0.17660 1393 2.45997E+02 6 0.52177 0.14205 1736 2.46591E+02 7 0.48524 0.11426 2164 2.47249E+02 8 0.45128 0.09190 2699 2.48044E+02 9 0.41969 0.07392 3338 2.46752E+02 10 0.39031 0.05946 4142 2.46282E+02 Centre of cavity gravity 12.371 9.891 -7.847 Nr of calcns/average/sigma volume 10 246.198 1.385 Inside > C1 RTL 200 @ 11.813 12.750 -5.950 Inside > C2 RTL 200 @ 11.812 13.896 -4.907 ... Inside > C15 RTL 200 @ 9.077 3.575 -11.205 Inside > O1 HOH 260 @ 16.834 7.214 -12.232 Lining > CE MET 10 @ 9.303 6.153 -1.218 Lining > ND2 ASN 13 @ 12.929 6.691 0.277 ... Lining > NE2 GLN 128 @ 12.436 5.329 -3.371 Lining > CZ PHE 130 @ 7.163 4.791 -3.985 Nr voxels/Voxel volume/Cavity volume on plot grid 1959 0.1250000 244.875
*** VOIDOO ***
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
We also have a plot file for every cavity:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 871 gerard rigel 21:07:29 cavity/crbpm26 > head -10 crbp_cav_1.ez2 EZD_MAP ! Created by VOIDOO V. 930825/2.4.2 at Tue Nov 16 21:29:51 1993 for user gerard CELL 50.000 50.000 50.000 90.000 90.000 90.000 ORIGIN 9 -1 -34 EXTENT 33 40 39 GRID 100 100 100 SCALE 1.000 MAP 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
And an O macro to draw the residues inside and surrounding each cavity:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 872 gerard rigel 21:07:29 cavity/crbpm26 > cat crbp_cav_1.omac ! Created by VOIDOO V. 930825/2.4.2 at Tue Nov 16 21:28:39 1993 for user gerard ! mol #Cavity-molecule name ?# ! centre_xyz 12.37121 9.891000 -7.847060 ! obj ins_1 zone 200 200 zone 260 260 end_object ! obj lin_1 zone 10 10 zone 13 13 zone 16 16 zone 19 19 zone 20 20 zone 23 23 zone 25 25 zone 29 29 ... zone 128 128 zone 130 130 end_object ! bell message Done ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present.
Created at Fri Dec 18 19:42:26 1998
by MAN2HTML version 971024/1.6