Double clicking on the following MolView files will launch MolView
and display the file.
The user can activate MolView with this file by dragging its
imageonto the MolView icon or by double-clicking it. If a MolView
file is already opened in MolView, it will be closed and this
file will be read. It is actually a ASCII file, but must be forced
open by programs such as MS Word since it is actually called a
'text' file rather than 'TEXT' file.
This is a PICT file created by MolView. MolView will open and
read this PICT file when it is dragged onto the MolView icon or
doubled-clicked. A new window opens without interferring with
other opened files. Up to two PICT files can be displayed at
one time in MolView. PICT files created by other programs can
also be displayed by MolView.
This is the icon for the new file format. It is a TEXT file and
the format of the data is discussed below. It acts much like
the old MolView files, but can be edited using any word processing
program or TeachText.
This is a QuickTime movie created by MolView. Up to two movies
can be played at at time in MolView, or the movie can be played
by many other programs on many different platforms. QuickTime
movies created by other applications can also be played by MolView.
a) MolView files created by another word processing program (see below for format)
b) PDB files ending with '.pdb', '.PDB', '.ent', or '.ENT'
c) Plot files created by the graphics program 'O'.
d) MOL files created by MolView or by another word processing program (see below)
e) Secondary structure files created by MolView or the user to be used in making ribbon diagrams.
f) 'names.pdb' file. This file, in the same directory as the application (if not there, MolView will make you hunt for it), contains a dictionary of residue names, atom names, van der Waal radii, and bonding distances. This can be edited as need by the user.
g) *.psiphi is a file made by MolView when the user asks MolView
to figure out where the helices, strands, and coils are. This
is a TEXT file that give the psi-phi (Ramachandran plot angles)
for each residue. Can be handy.
MolView preference file. This controls many of the display and
modeling parameters (e.g. stereo diveregence, bonding distance
criteria, etc.)If MolView can figure out where your System folder
is, it will write it there when you quit the program. If not,
it will place it in your local folder. You can, in the preference
dialog window, write and read this file anywhere you wish.
To see these some of these icons, you may have to rebuild your desktop after installing the program .
Note: All coordinates are fixed and not changed by MolView.
When displayed on the screen, MolView applies the rotation matrix
while drawing. Therefore, when you write out a new MolView file,
the coordinates are exactly the same - making it rather unecessary
to write out updated MolView files. Instead, you should probably
just write out the smaller MOL object files that are very handy
to use.
MolView_Format_3
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
REMARK FILENAME=/usr/alf/tom/Toxin_refine/slowcool_wat.pdb
REMARK TOPH19.pep -MACRO for protein sequence
ATOM CB LEU 1 26.227 48.526 41.551 18.90
ATOM CG LEU 1 26.566 47.061 41.243 18.26
ATOM CD1 LEU 1 26.228 46.146 42.391 17.57
ATOM CD2 LEU 1 25.814 46.636 40.003 20.64
ATOM C LEU 1 28.107 48.686 43.243 23.05
MOL
26.227 48.526 41.551 0
26.566 47.061 41.243 1
26.228 46.146 42.391 1
25.814 46.636 40.003 1
Line #1: This must contain the name 'MolView_Format_3'
Line #2, 3, 4: This is the orientation matrix, and something
is required. By default, the identity matrix shown here (no rotation)
is used.
REMARK These lines are not read now, but will be in the near
future.
ATOM This key word designates that an atomic coordinate follows
in this line. Atomic coordinates are not necessary in this file
(but are required for many of MolView functions). The following
input is all free-format (i.e. you just need a space between each
number or string). Following the word 'ATOM' is the
atom type, the amino acid (or residue) type, the residue number,
the x, y, and z coordinates, and finally the B value (the motion
or thermal factor measure in square angstroms).
MOL This word designates that a MOL object is to follow. These
are not necessary in the file and there can be up to 30 of these
MOL objects in the file. In the lines that follow are the x,
y, z coordinates for a point in the line followed by a '0'
for a moveto command or a '1' for a drawto command.
A moveto command is as if the pen is picked up and moved to that
x,y,z coordinate and a drawto command is as if the pen is put
down on the paper and a line is drawn to that position. This
easy format allows the user to really make any kind of 3D drawing
that they want. This is basically the format of the follow MOL
object file that follows.
MOL
COLOR 65535 0 0
-9.847501 3.826999 12.170001 0
-6.035501 3.627002 12.081000 1
-3.618501 0.900001 10.902999 1
-5.622500 -2.282998 10.205001 1
-5.663501 -5.520001 8.198001 1
-9.074500 -5.023999 6.588000 1
-9.508500 -6.050000 2.958999 1
MOL
COLOR 65535 0 0
-9.847501 3.826999 12.170001 0
-6.035501 3.627002 12.081000 1
-3.618501 0.900001 10.902999 1
-5.622500 -2.282998 10.205001 1
-5.663501 -5.520001 8.198001 1
-9.074500 -5.023999 6.588000 1
-9.508500 -6.050000 2.958999 1
MOL This word designates that a MOL object is to follow, and
designates when one MOL object stops and a new one starts. Again,
up to 30 MOL objects can be displayed by MolView at one time.
COLOR This word designates that the red, green, and blue values
are to follow (optional input). If this line is not inputted,
then MolView will pick out your colors. If you used MolView to
create and write out this file, then this color will be automatically
written to this file. The values for the colors range from 0
to 65535. For example; black = 0 0 0, red = 65535 0 0, white
= 65535 65535 65535, yellow = 65535 65535 0, and grey = 30000
30000 30000.
The remaining lines are the x, y, z coordinates and a 0 for a
moveto or a 1 for a drawto command. Input for each MOL object
is terminated by the word 'MOL' or the end of the
file.
These are like snippits of atomic models that can be dragged onto
an open MolView file or opened on their own without any atomic
coordinates.s Since all coordinates are absolute, alignment is
always perfect. Note that there is not an orientation matrix
stored in these objects. The orientation is determined by the
MolView file or by the user during the current execution of the
program. I felt it would be way too confusing to have the model
spin around as each different MOL object is added to the screen.
3) *.struc File (TEXT file type, any creator, any file name):
coil 1 2
sheet 3 5
coil 5 8
helix 9 14
coil 15 17
helix 18 28
coil 29 31
sheet 32 35
coil 36 40
sheet 41 44
This is just a free format file that contains a list of the secondary
structural elements: coil for random coil, sheet for beta-sheet,
and helix for alpha-helix. This file can be created by a) MolView
when creating a ribbon diagram, b) by MolView when reading a Brookhaven
(PDB) coordinate list, or c) by the user using any common TEXT
editor.
4) 'names.pdb' File (TEXT file type, any creator):
RESIDUES
RTL
F6P
ALA
GLU
ARG
LEU
MOF
STOP
ATOMS
ZN
HOH
N
CO
CA
STOP
CPK_Radii
C 1.54
N 1.5
O 1.4
H 1.2
STOP
Bond_Distances
C C 1.2 1.99
C N 1.2 1.99
C O 1.2 1.99
C H 0.8 1.1
N H 0.8 1.1
H H 0.8 0.95
O H 0.8 1.1
STOP
This is just a free format file that contains a dictionary of
atom names, residue names, and distances. If you see a ??? for
an atom name in your model when displayed in MolView, it means
that MolView cannot find that name in this list. Just find that
name and add it to this list. MolView uses this list to save
on memory and needs it to properly draw the models.
RESIDUES This is a list, terminated by the word 'STOP'
of possible residues (e.g. ALA, GLU, etc.)
ATOMS This is a list, terminated by the word 'STOP'
of possible atoms.
CPK_Radii A list of atoms and their van der Waal radii.
Bond_Distances In each line are two atom types followed by a minimum
and maximum distance that defines a chemical bond for these types
of atoms.