Program : MAPROP
Version : 950118
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 : calculate properties on a grid
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.
940317 - 0.1 - initial version & documentation
940318 - 0.2 - removed bug; minor changes
940320 - 0.3 - added RESET constant; made 'radii' library
940419 - 0.4 - started option "NEST" (requires more work later)
950118 - 0.5 - sensitive to environment variable GKLIB
MAPROP is a simple program to calculate properties of
molecules on a grid. For example, you can generate a
map with the electrostatic potential for each grid
point, or a map which contains the element number of
the nearest atom.
Depending on the library file and parameters that you
feed into the program, you can calculate all sorts
of grid-based properties.
One day, O may contain an option to colour a map
depending on the value for that grid point in some
other map. Then, it will be trivial to colour-code
a van der Waals surface by the type of the nearest
atom or residue, for example. Until that day, the
most useful application of MAPROP will probably be
in calculating electrostatic potential and polarity
or hydrophobicity maps.
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
The following input is required:
(1) a library which contains values of any property for the atoms that occur in your molecule. The format for such files is identical to that of VOIDOO library files (see the VOIDOO manual). Property values may be listed for chemical elements, specific atoms or residue/atom-type combinations. In addition, the file must contain a list of residue types which are to be used by MAPROP (residues not occurring in this list are rejected on input).
(2) a structure in the form of a PDB file.
(3) parameters for the grid calculations: the following map P(X) will be calculated, where, for each atom A and each grid point X, R = distance(A,X):
IF R > Cutoff => no contribution
IF R < Cuton => P(X) = P(A) * C
ELSE => P(X) = P(A) * C / (R^N)
All points which are NOT set, will be given a value Q
C is a constant and N and integer power (.., -1, 0, 1, 2, ..) to which the distance should be raised.
Values for different atoms A near X may be combined:
SUM -> sum all values from contributing atoms
PROD -> multiply them
MIN -> take the minimum
MAX -> take the maximum
NEAR -> only keep value of the nearest atom
(4) the grid spacing for the output map (in A). The map will be in New EZD format. This means that it can be read and displayed by O directly, or mappaged with MAPMAN. The grid will be such that it encompasses your molecule, and a margin of (CUTOFF + 1.0) A will be added on all sides (but never less than 3 A, or more than 10 A).
First, the grid will be initialised. The initial value depends on the combination option you have chosen: for NEAR and SUM this value is 0.0, for PROD 1.0, for MIN 999999.999 and for MAX -999999.999. The distance map (to encode the shortest distance of a grid point to any atom in the case of NEAR, and to record if a grid point has been given a value in the other cases) is initialised with a value of 999999.999.
Second, the map is calculated. A loop is carried out over all atoms. For each atom, the part of the map which can be affected by it (depends on its position in space and the value of CUTOFF) is delineated and all grid points are tested to check their distance. Depending on the distance and the type of combination you selected, the corresponding value in the map is updated appropriately. A message is printed every 500 atoms so you know the program is still working. Afterwards, all map points which were not set that you (i.e., not close enough to any atom) are reset to a value supplied. Some statistics of the map are printed and, finally, it is written to a file (note that a dummy cell is introduced by MAPROP).
The map is written is new EZD format. Some CPU time is spent to minimise the amount of disk space occupied by the file (by removing zeroes behind the decimal point, and by replacing multiple spaces by only one space). Although this takes some time (but only once !), it reduces the file size by typically 50 % or more.
Now, the map can be read by MAPMAN, multiplied by -1.0 in some cases, and mappaged. All you have to do now, is to centre on your molecule and draw the map(s) !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 364 gerard rigel 21:16:43 scratch/gerard > run maprop... Run maprop
... Executing /nfs/public/IRIX/bin/4d_maprop ... For gerard on rigel at Sun Mar 20 21:17:24 MET 1994
*** MAPROP *** MAPROP *** MAPROP *** MAPROP *** MAPROP *** MAPROP ***
Version - 940320/0.3 (C) 1993/4 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 - Sun Mar 20 21:17:24 1994 User - gerard Mode - interactive Host - rigel ProcID - 10380 Tty - /dev/ttyq1
*** MAPROP *** MAPROP *** MAPROP *** MAPROP *** MAPROP *** MAPROP ***
***** MAPROP ***** MAPROP ***** MAPROP ***** MAPROP ***** MAPROP *****
Current version : 940320/0.3 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 points for map : 8388608 Ditto, for distance buffer : 8388608 Memory use (Bytes) for major arrays : 67908864
***** MAPROP ***** MAPROP ***** MAPROP ***** MAPROP ***** MAPROP *****
Data input ----------
(1) Property values and residue types
Library file ? (maprop.lib) /home/gerard/progs/maprop/maprop.charges
Reading your library file ... Nr of lines in library file : ( 143) Nr of elements defined : ( 14) Nr of atom types defined : ( 4) Nr of residue/atom types : ( 46) Nr of residue types defined : ( 24)
ELEM N 1.00 C 0.00 O -1.00 S 0.00 ELEM H 0.00 P 0.00 NA 1.00 MG 2.00 ELEM CL -1.00 CA 2.00 MN 2.00 FE 2.00 ELEM ZN 2.00 CD 2.00
ATOM N -0.10 C 0.55 O -0.55 CA 0.10
SPAT ARG CD 0.10 ARG NE -0.10 ARG CZ 0.50 ARG NH1 0.25 SPAT ARG NH2 0.25 ASN CG 0.55 ASN OD1 -0.55 ASN ND2 0.00 SPAT ASP CB -0.16 ASP CG 0.36 ASP OD1 -0.60 ASP OD2 -0.60 SPAT CYS CB 0.19 CYS SG -0.19 GLN CD 0.55 GLN OE1 -0.55 SPAT GLN NE2 0.00 GLU CG -0.16 GLU CD 0.36 GLU OE1 -0.60 SPAT GLU OE2 -0.60 HIS CB 0.10 HIS CG 0.15 HIS CD2 0.20 SPAT HIS ND1 0.05 HIS CE1 0.45 HIS NE2 0.05 LYS CE 0.25 SPAT LYS NZ 0.75 MET CG 0.06 MET SD -0.12 MET CE 0.06 SPAT PRO N -0.20 PRO CD 0.10 SER CB 0.25 SER OG -0.25 SPAT THR CB 0.25 THR OG1 -0.25 TRP CG -0.03 TRP CD1 0.06 SPAT TRP CD2 0.10 TRP NE1 -0.06 TRP CE2 -0.04 TRP CE3 -0.03 SPAT TYR CZ 0.25 TYR OH -0.25
RESI ALA ARG ASN ASP CYS GLN GLU GLY RESI HIS ILE LEU LYS MET PHE PRO SER RESI THR TRP TYR VAL CPR CYH PYR PCA
(2) PDB file
PDB file name ? (in.pdb) a16.pdb
Reading your PDB file ... REMARK WRITTEN BY O VERSION 5.9.1 REMARK SAT SEP 18 01:38:23 1993 Number of atoms read : ( 3220) Number of atoms kept : ( 3220) Number of atoms rejected : ( 0) No residue types rejected
(3) Various parameters
The following map P(X) will be calculated:
For each atom A and each grid point X, R = distance(A,X):
IF R > Cutoff => no contribution IF R < Cuton => P(X) = P(A) * C ELSE => P(X) = P(A) * C / (R^N)
All points which are NOT set, will be given a value Q
Values for different atoms A may be combined: SUM -> sum all values from contributing atoms PROD -> multiply them MIN -> take the minimum MAX -> take the maximum NEAR -> only keep value of the nearest atom
Minimal radius CUTON (>0) ? ( 1.000) 1 Minimal radius CUTON : ( 1.000E+00) Maximal radius CUTOFF (>CUTON) ? ( 7.000) 10 Maximal radius CUTOFF : ( 1.000E+01) Constant C (<> 0) ? ( 1.000) 1 Constant C : ( 1.000E+00) Radius power N ? ( 1) 1 Radius power N : ( 1) Uniform value for unset points ? ( 0.000) 0 Uniform value for unset points : ( 0.000E+00) Combine SUM/PROD/MIN/MAX/NEAR ? (SUM) SUM Combination method : (SUM) Name of map file (NEWEZD) ? (maprop.nezd) sgi.nezd Name of map file (NEWEZD) : (sgi.nezd)
(4) Map grid
Min, max, cog for X : 5.228 54.913 30.107 Min, max, cog for Y : 40.635 86.626 63.884 Min, max, cog for Z : 26.399 91.680 61.070 Grid spacing (A) ? ( 1.000) Grid spacing (A) : ( 1.000) Margin on all sides (A) : ( 10.000) Min, max, cog for X : -5.000 65.000 Min, max, cog for Y : 29.000 97.000 Min, max, cog for Z : 15.000 102.000 Number of grid points : ( 71 69 88) Required buffer : ( 431112) Buffer size : ( 8388608) % of buffer needed : ( 5.139) Volume per voxel (A3) : ( 1.000E+00)
Data input done ---------------
1 CPU total/user/sys : 3.4 3.0 0.4
Clearing nearest atom buffer ...
2 CPU total/user/sys : 0.3 0.3 0.0
Initialising map with value : ( 0.000E+00)
3 CPU total/user/sys : 0.4 0.3 0.1
Calculating map ... Nr of atoms done : ( 500) Nr of atoms done : ( 500) Nr of atoms done : ( 1000) Nr of atoms done : ( 1500) Nr of atoms done : ( 2000) Nr of atoms done : ( 2500) Nr of atoms done : ( 3000)
4 CPU total/user/sys : 182.2 178.2 4.0
Resetting unset points to : ( 0.000E+00) Nr of points reset : ( 250437) Out of a total of : ( 431112)
Nr of points in grid : ( 431112) Sum of values in map : ( -1.346E+04) Average value in map : ( -3.121E-02) St. Deviation : ( 1.231E-01) Minimum value in map : ( -1.496E+00) Maximum value in map : ( 1.177E+00)
5 CPU total/user/sys : 1.7 1.6 0.1
Opening New-EZD map file ...
Writing map ... CELL 200.000 200.000 200.000 90.000 90.000 90.000 ORIGIN -5 29 15 EXTENT 71 69 88 GRID 200 200 200 SCALE 1.000
6 CPU total/user/sys : 111.9 109.7 2.2
*** MAPROP *** MAPROP *** MAPROP *** MAPROP *** MAPROP *** MAPROP ***
Version - 940320/0.3 Started - Sun Mar 20 21:17:24 1994 Stopped - Sun Mar 20 21:23:32 1994
CPU-time taken : User - 293.0 Sys - 6.9 Total - 299.9
*** MAPROP *** MAPROP *** MAPROP *** MAPROP *** MAPROP *** MAPROP ***
>>> This program (C) 1993-94, GJ Kleywegt & TA Jones <<< E-mail: "gerard@xray.bmc.uu.se" or "alwyn@xray.bmc.uu.se"
*** MAPROP *** MAPROP *** MAPROP *** MAPROP *** MAPROP *** MAPROP ***
STOP ... Toodle pip ... statement executed
real 6:08.3 user 4:53.0 sys 6.9
... Started Sun Mar 20 21:17:24 MET 1994 ... Finished Sun Mar 20 21:23:32 MET 1994 ... Mode Normal
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMA maprop.charges - atomic charge library used by program MAPROP REMA - values from XPLOR tophcsdx.pro ... ELEM ' N' 1.0 ELEM ' C' 0.0 ELEM ' O' -1.0 ELEM ' S' 0.0 ELEM ' H' 0.0 ELEM ' P' 0.0 REMA ELEM 'NA' 1.0 ELEM 'MG' 2.0 ... ATOM ' N ' -0.1 ATOM ' C ' 0.55 ATOM ' O ' -0.55 ATOM ' CA ' 0.1 ... SPAT 'ARG* CD ' 0.1 SPAT 'ARG* NE ' -0.1 SPAT 'ARG* CZ ' 0.5 SPAT 'ARG* NH1' 0.25 SPAT 'ARG* NH2' 0.25 REMA SPAT 'ASN* CG ' 0.55 SPAT 'ASN* OD1' -0.55 SPAT 'ASN* ND2' 0.0 ... SPAT 'TYR* CZ ' 0.25 SPAT 'TYR* OH ' -0.25 ... RESI 'ALA' RESI 'ARG' RESI 'ASN' RESI 'ASP' ... RESI 'VAL' RESI 'CPR' RESI 'CYH' RESI 'PYR' RESI 'PCA' END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMA maprop.atypes - atomic type library used by program MAPROP ... ELEM ' N' 7.0 ELEM ' C' 6.0 ELEM ' O' 8.0 ELEM ' S' 16.0 ELEM ' H' 1.0 ELEM ' P' 15.0 ... RESI 'ALA' RESI 'ARG' ... RESI 'PCA' END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMA maprop.polar - "polarity" library used by program MAPROP REMA - code: polar +1, hydrophobic -1, rest 0 ... ELEM ' N' 1.0 ELEM ' C' -1.0 ELEM ' O' 1.0 ELEM ' S' 0.0 ELEM ' H' 0.0 ELEM ' P' 0.0 ... ATOM ' N ' 1.0 ATOM ' C ' 0.0 ATOM ' O ' 1.0 ATOM ' CA ' -1.0 ... SPAT 'ARG* CD ' 0.0 SPAT 'ARG* CZ ' 0.0 ... SPAT 'TYR* CZ ' 0.0 ... RESI 'ALA' RESI 'ARG' ... RESI 'PCA' END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMA maprop.radii - library used by program MAPROP to mimick REMA the method of Voorintholt et al. to display REMA surfaces, cavities, clefts, tunnels etc. ... ELEM ' N' 1.0 ELEM ' C' 1.0 ELEM ' O' 1.0 ELEM ' S' 1.0 ELEM ' H' 1.0 ELEM ' P' 1.0 ... RESI 'ALA' RESI 'ARG' ... RESI 'PCA' END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- speed: the algorithm scales up linearly with the number of atoms, and with the third power of the reciprocal grid spacing as well as the third power of the cut-off radius. If the radius power N is unequal zero, a square root has to be evaluated for every grid point. If the power is -2, -1, 1 or 2, the formula is explicit; otherwise (RADIUS**POWER) is explicitly evaluated.
- timing: identical runs on an ESV, R3000 SGI/Indigo and a DEC/Alpha (3220 atoms, calculating electrostatic potential, cut-on 1.0, cut-off 10.0, power 1, SUM method, reset value 0.0, grid spacing 1.0 A yielding 431,112 grid points of which 250437 were reset afterwards) require the following amounts of CPU time (user/system time):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
ESV SGI ALPHA
----------- ----------- -----------
map calculation 247.9 / 0.1 178.2 / 4.0 61.4 / 0.3
map output 222.5 / 1.1 109.7 / 2.2 32.9 / 4.5
total for the run 478.0 / 2.0 293.0 / 6.6 95.4 / 5.0
speed-up vs. ESV 1.0 1.6 5.0
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Other than in the header line, there were no differences between the resulting EZD files.
- MAPMAN, MAMA and IMP are part of the RAVE package; LSQMAN is part of the DEJAVU package
- if you create new library files for calculating other properties, please send them to me for redistribution to other users
- if you would like to see changes to the map-calculation formula, or more of them, let me know
None, at present.
Created at Fri Dec 18 19:42:16 1998
by MAN2HTML version 971024/1.6