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README
~~~~~~
for 'code-mbg' library code (1.1)
A Overview
~~~~~~~~
This is "library" source code for doing a variety of calculations on
protein structures and sequences, including calculating surface areas
and volumes, superimposing two structures, calculating helix axes,
finding H-bonds and contacts, and computing sequence similarity.
The primary use of this computer code is for volume or surface
calculations. If you use it for calculating volumes, please refer to
the following references:
M Gerstein, J Tsai & M Levitt (1995). "The volume of atoms on the
protein surface: Calculated from simulation, using Voronoi polyhedra,"
J. Mol. Biol. 249: 955-966.
Y Harpaz, M Gerstein & C Chothia (1994). "Volume Changes on Protein
Folding," Structure 2: 641-649.
If you use the code for other purposes (such as calculating surfaces
areas or helix axes), please cite:
M Gerstein (1992). "A Resolution-Sensitive Procedure for Comparing
Protein Surfaces and its Application to the Comparison of
Antigen-Combining Sites," Acta Cryst. A48: 271-276.
B Copying, Building, Using...
~~~~~~~~~~~~~~~~~~~~~~~~
This code was assembled by Mark Gerstein. Much of it was written by
Mark Gerstein but there are substantial contributions from Yehouda
Harpaz, Jerry Tsai, David Hinds, and others.
This code is copyright 1995. You are free to use it for whatever
academic calculations you may wish to. However, you are asked to:
1 -- Cite the references above when you use the programs for published
work;
2 -- Keep this statement with the programs;
3 -- Not incorporate this code into any commercial programs without
obtaining explicit permission from the author.
Contact Mark Gerstein <mbg@hyper.stanford.edu> if you have any
questions or difficulties.
Everything here is written in the C language and compiles using make
under unix. It has so far been tested on DEC alphas, SG Indigos, and
an i486 running linux. To get everything going, just type 'make' in
the top level directory and all the libraries and executables should
be built and tested. The actual library source is contained in the
subdirectory 'src-lib' . The subdirectory 'data' contains various data
files pertinent to the calculations -- e.g. standard radii and volumes
for atoms (See the paper for more explanation of the parameters).
The calculations of most interest to people will be those relating to
Voronoi volumes. For these a few jiffy demonstration programs are
built from the library code. These are contained in the subdirectory
'src-prog' . The programs for calculating surfaces and volumes are
based on Fred Richards' original surface and volume programs, written
in fortran. These are available from Fred Richards at Yale (See F M
Richards (1974), J. Mol. Biol. 82: 1-14; F M Richards (1977),
Annu. Rev. Biophys. Bioeng. 6: 151-176).
C Descriptions of the sample executables
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Descriptions of some of the executables in the sub-directory
'src-prog' follow. Sample runs are in the directory 'sample-runs'. In
this discussion, the following convention is used. (To keep the
distribution from getting to big the sample run for the
full-dump-polyhedra program is abbreviated.)
in.pdb = input file in pdb format ("-" for stdin).
out.pdb = output file in pdb-like format with extra columns and results
written into various columns
[-arg] = an optional argument
------------
calc-surface.exe -i in.pdb > out.pdb
------------
* Surface *
ATOM 1 N ARG 1 32.231 15.281 -13.143 0.00 0.00 50.43
(Surface is in square Angstroms.)
-----------
calc-volume.exe -i in.pdb [-method N] [-RichardsRadii] > out.pdb
-----------
First optional argument determines whether the normal Voronoi, method
B, the radical plane, or a modified method B is used. Inclusion of
second optional argument causes Richards' radii to be used for the
atoms. The default is the radii of Chothia. (See paper for
discussion.)
* Volume *
ATOM 2 CA ARG 1 32.184 14.697 -11.772 0.00 0.00 15.25 0
(Volume is in cubic Angstroms. If volume isn't calculable, it is set to -1.00)
--------------
show-2rad-refV.exe -i in.pdb [-sv ref-vol.dat] > out.pdb
--------------
Optional argument "-sv" specifies a file for the reference volumes.
R-Cov R-VDW V-Ref
ATOM 1 N ARG 1 32.231 15.281 -13.143 0.70 1.65 13.63
R-Cov = covalent radius (A) (Different parameters are possible;
R-VDW = VDW radius (A) see JMB paper above.)
V-Ref = Standard reference volume (cubic A) from the analysis of the interiors
of proteins (See JMB paper above for discussion.)
--------------
dump-polyhedra.exe -i in.pdb > out.vects
--------------
This dumps the vertices of the Voronoi polyhedron for each atom in
format suitable for import into the graphics program O. Here is a
section of out.vects.
DRAW_OBJECT_WritePoly t ChangeThisToTotalLines 80
Begin_object WritePoly
! Beginning Atom C ARG 1
Move 38.9047 18.7797 -13.1947
Line 32.9549 13.8252 -13.0297
Move 32.9549 13.8252 -13.0297
Line 32.4831 13.2205 -12.7607
Move 32.4831 13.2205 -12.7607
Line 32.8308 11.9338 -10.8669
Move 32.8308 11.9338 -10.8669
.
.
.
Line 34.1948 12.8591 -10.6045
Move 33.1069 12.4968 -10.2644
Line 32.3484 12.5938 -10.1057
Move 32.3484 12.5938 -10.1057
Line 32.8308 11.9338 -10.8669
Move 32.8308 11.9338 -10.8669
Line 33.2656 12.1306 -10.6793
Move 33.1069 12.4968 -10.2644
Line 33.2656 12.1306 -10.6793
! volume= 14.1673 MaxDistSq= 7.5539
! Ending Atom 2 : C ARG 1
! ATOM 3 C ARG 1 33.438 13.890 -11.387 14.17 7.55
... and so on ...
End_Object
To use this with O, do the following:
1. Change the '80' on the first line of the output to the
number of lines in out.vects.
2. Inside of O, type 'read_formatted out.vects' to create
an O datablock 'draw_object_writepoly' .
3. Then type 'draw_object draw_object_writepoly' to
draw this datablock to the screen using the O graphics
descriptor language.
-------------------
full-dump-polyhedra.exe -i in.pdb > out.dat
-------------------
Here out.dat contains a full specification of the polyhedron for each
atom, including the area of each face and the vertices constituting
it. This full specification is very useful for quantifying
inter-atomic contacts and generating the Delaunay tessellation (see
below). For instance, for the first atom, the CA of Arg2, the
polyhedron description is shown below. Atoms are specified by the ISER
number (the first number after the "ATOM").
FullDumpPoly(): BEGIN polyhedron for following atom, which has ID 2.
ATOM 2 CA ARG 1 32.184 14.697 -11.772 0.00 0.00
DumpAFace(): BEGIN face 0
-- Face between atom 2 and neighbour 1, which are separated by 1.491 A
-- List of 5 vertices: number, derived from atoms (4 IDs), coord. (x,y,z)
0 2 6 1 5 31.6946 13.6065 -13.1026
1 2 6 1 3 32.5716 13.1079 -13.2849
2 2 33 1 3 34.5954 17.0962 -11.5166
3 2 872 1 33 31.6729 18.7648 -10.9061
4 2 872 1 5 29.9060 17.9477 -11.3147
-- Face-Centroid= 32.0881 16.1046 -12.0250
-- Distance of face to central atom: 1.4334
-- Face-Area= 8.4958 Pyramid-Volume= 4.0592
DumpAFace(): END face 0
DumpAFace(): BEGIN face 1
-- Face between atom 2 and neighbour 5, which are separated by 1.531 A
-- List of 5 vertices: number, derived from atoms (4 IDs), coord. (x,y,z)
0 2 6 1 5 31.6946 13.6065 -13.1026
.... and so on .... and on ....
*** ***
*** This program effectively describes the Delauney Tessellation. ***
*** ***
The Delauney tessellation is formed from connecting the two atoms that
determine each face. (That's why it's dual to the Voronoi polyhedron).
Specifically, if you look at the output, you will see a lot of lines
like:
-- Face between atom 2 and neighbour 5, which are separated by 1.549 A
-- Face between atom 2 and neighbour 3, which are separated by 1.497 A
-- Face between atom 7 and neighbour 438, which are separated by 3.455 A
The two atom numbers on each line (e.g. 2 and 5 for the first line
above) are serial numbers (ISER in PDB terminology) of a pair of atoms
connected in the Delauney tessellation. So if you take the output
above and draw a vector between atoms 2 and 5, 2 and 3, and 7 and 438,
you will begin to build up the tessellation.
D Location of the code
~~~~~~~~~~~~~~~~~~~~
This file and all the computer code is located at the following URLs:
1 ftp://hyper.stanford.edu/pub/mbg/SurfaceVolumes/code-mbg.tar.Z
This URL is a tar achive that contains the source code plus sample
output and scripts for checking out the programs. To extract files
from the archive use the command
'uncompress -c code-mbg.tar.Z | tar xvf -'
2 ftp://hyper.stanford.edu/pub/mbg/SurfaceVolumes/code-mbg
This URL has everything in the above archive expanded into
directories. It also has pre-built libraries and executables for DEC
alpha, Silicon Graphics, and i486 linux computers. (These binaries are
stored in the subdirectories lib-alpha, lib-sgi, lib-linux, bin-alpha,
bin-sgi, and bin-linux . Note that 'lib' and 'bin' are just arbitrary
pointers to an appropriate pair of these directories.)
Mark Gerstein <mbg@hyper.stanford.edu> / 25 October 1995 / Stanford, CA
.. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ ..
E Other References
~~~~~~~~~~~~~~~~
Regarding surfaces and volumes, you may also want to look at:
M Gerstein & C Chothia (1996). "Packing at the Protein-Water Interface"
PNAS 93: 10167-10172.
M Gerstein & R M Lynden-Bell (1993). "What is the natural boundary
for a protein in solution?" J. Mol. Biol. 230: 641-650.
F History
~~~~~~~
25 October 1995 -- Version 1.0, released code
3 May 1996 -- Version 1.1,
* Corrected bug that prevented the calculation of hydrogen
volumes
* Corrected bug (I think) that lead to the first atom type being
given a zero radius. To make doubly sure this doesn't happen,
just make this first atom type a dummy type ("JUNK").
7 June 1996 -- Version 1.101
* Added a few references to this README
26 November 1996 -- Version 1.102
* Fixed typing of GLY CA (was C4H, now C4HH)
24 December 1996 -- Version 1.103
* Updated this README file to better document the
calculation of Delauney Tessellations