RasMol/Raster 3D question
Ross J. Reedstrom
ross at repressor.pharmacy.wisc.edu
Mon Mar 11 11:19:48 EST 1996
On Mon, 11 Mar 1996, Bernard Murray wrote:
> Hello all,
> I'm using RasMol 2.5 under Windows 3.1 and am hoping to colour
> parts of molecules by manipulation of PDB format files. One possible
The COLO fields are an extension to PDB format orginially invented by
David Bacon for Raster3D. They documented in the Raster3D docs somewhere,
but also in the RasMol 2.5 docs you have right there - I believe it's an
MS-Write file called manual.doc. - Here's an excerpt:
PDB Colour Scheme Specification
RasMol also accepts the supplementary COLO record type in the PDB files.
This record format was introduced by David Bacon's Raster3D program for
specifying the colour scheme to be used when rendering the molecule.
This extension is not currently supported by Brookhaven. The COLO record
has the same basic record type as the ATOM and HETATM records described
Colours are assigned to atoms using a matching process. The Mask field
is used in the matching process as follows. First RasMol reads in and
remembers all the ATOM, HETA and COLO records in input order. When the
user-defined ('User') colour scheme is selected, RasMol goes through
each remembered ATOM/HETA record in turn, and searches for a COLO record
that matches in all of columns 7 through 30. The first such COLO record
to be found determines the colour and radius of the atom.
1-6 'COLOR' or 'COLOUR'
7-30 Mask (described below)
31-38 Red component
39-46 Green component
47-54 Blue component
55-60 Sphere radius in Angstroms
Note that the Red, Green and Blue components are in the same positions
as the X, Y, and Z components of an ATOM or HETA record, and the van der
Waals radius goes in the place of the Occupancy. The Red, Green and Blue
components must all be in the range 0 to 1.
In order that one COLO record can provide colour and radius
specifications for more than one atom (e.g. based on residue, atom type,
or any other criterion for which labels can be given somewhere in
columns 7 through 30), a 'don't-care' character, the hash mark "#"
(number or sharp sign) is used. This character, when found in a COLO
record, matches any character in the corresponding column in a ATOM/HETA
record. All other characters must match identically to count as a match.
As an extension to the specification, any atom that fails to match a
COLO record is displayed in white.
Ross J. Reedstrom
rjr at pharmacy.wisc.edu (608) 265-5591
School of Pharmacy or
University of Wisconsin-Madison (608) 265-2599
425 N. Charter St.
Madison, WI 53706
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