1. Overview
Cmoil, read as see-moil, is a program written in C++ to view mutiple molecular structures
from connectivity and coordinate files. The coordinate files can be in CRD, DCD, or PATH
format if the connectivity file is provided at same time. The program can also display
structure from PDB file directly or plot coordinates according to a XYZ format file.
With cmoil, user can generated animated gif graph file or mpeg movie for web publishing.
Cmoil provides structural information for selected atoms through residue selecting and
atom level color setting.
Cmoil supports structure overlap with selectable atom alignments.
Cmoil also supports ribbon, secondary structure, and protein surface display.
Cmoil now has a simple menubar for quick viewing switch.
2. Input Parameters
The program takes instruction files as input. All parameters are read from instruction
files for display control. For those coordinate files in either PDB or XYZ format,
cmoil also takes coordinate file as input argument for quick viewing, such as
"cmoil -pdb 1lh1.pdb" or "cmoil -xyz example.xyz".
The parameters in an instruction file are defined as following:
syntax Description
------------------------- --------------------------------------------------------------
connfile= ; connectivity file
crdfile= ; coordinate file in CRD format (CHARMM) or
pthfile= ; coordinate file in PATH format or
dcdfile= ; coordinate file in DCD format or
pdbfile= ; coordinate file in PDB format or
xyzfile= ; coordinate file in XYZ format
dispmode1= ; atom display mode :
stick -- stick mode
stickball -- stick-ball mode
space -- spaceball filling mode
dispmode2= ; structure display mode :
backbone -- show Ca backbone
ribbon -- show ribbon
structure -- show secondary structure
dispmode3=surface ; show protein surface
surfprobe= ; probe to build a surface, default is 1.4A as using water
regeneratevtxfile=<0|1> ; set to 1 if sufprobe changes to regenerate surface vertex file
(following parameters are optional)
nostruct= ; number of structures in a PATH/DCD file
bondbuild=<0|1> ; Caculate bonds
swapmode=<0|1> ; default=0 which is no swap. 1 swap binary PATH or DCD file
skipres= ; residues not to display
stickmode= ; residues displayed in stick mode
spacemode= ; residues displayed in spaceball filling mode
ribbonmode= ; residues displayed in ribbonmode mode
colorsetting= ; setup atom color, use multiple rows to setup atom colors
; for different color value. It is following basic pick
; syntax with "" color value, e.g. :
; colorsetting=chem prtc CA | chem prtc CB <8-124-325>
; colorsetting=chem prtc O <487-0-0>
ribboncolor= ; use pick syntex to set backbone/ribbon/secondary structure colors
alignsetting= ; use pick syntax to setup alignment for structure overlap
; e.g. alignsetting=chem mono ALA | #mon 3 4
; Default is to use CA for overlapping.
sleepseconds= ; pause between each frame in movie mode
maxframes= ; number of frames save to image file
imagetype= ; image file type, single gif, mpg, or mutiple bmp and png file(s)
gifloops= ; loops for gif file
bmpfile= ; image file to save
------------------------------------------------------------------------------------------
3. Display Control
Cmoil has three modes: DISPLAY, MOVIE, and PICK.
Cmoil is in DISPLAY mode by default. There are some keyboard commands that are active in
a graphic window, which are also available from manu option:
m: display structures in a MOVIE mode for coordinates in path or dcd format
or switch back from MOVIE mode to DISPLAY mode
a: advance to next structure in DISPLAY mode for path input, or
display single model for an PDB input
c: display single chain for an PDB input
p: enter/quit PICK mode for detail structural information. Use left button to select
atoms. The coordinates and radius of a selected atom are displayed. For a PDB input,
the radius is estimated. If an PDB atom cannot be identified, the radius is set to
1.0. Then use following keys to display caculated results:
d: display distance between last selected two atoms;
a: display angle of last selected three atoms;
t: display torsional angle of last selected four atoms.
Atom names are displayed as
[struct_name]:#structure:residue_seq_number:residue_name:atom_name
for binary coordinate files, or as
[struct_name]:[model serial]:chain id:residue_seq_number:residue_name:atom_name
when any PDB input file is envolved, or as
[struct_name]:residue_seq_number:residue_name:atom_name
for any other file formats. The fields in [] can be silent when no confusion is
caused.
In PICK mode, you can also make instant color changes with following keys, the
changed colors are displayed under select yellow points:
+: make the atom brighter
-: make the atom darker
^: reverse color of the atom
r: more red for the atom
g: more green for the atom
b: more blue for the atom
R: less red for the atom
G: less green for the atom
B: less blue for the atom
Those color changes are NOT saved.
s: save the picture into a bitmap file for single structure image. The bitmap
file will have the same path and base name as of the connectivity file and have a
suffix of ".bmp". If the dispaly is in movie mode, an animated GIF image file, or
a MPEG movie file, or a group of sequenced bmp or png image files will be saved at
the metioned directory upon user's choice. Cmoil uses following libraries/packages
to save or convert image formats:
ImageMagick: copyrighted by ImageMagick Studio,
gifmerge: written by M. Podlipec, and
mpeg2endcode: provided by "MPEG Software Simulation Group".
User can publish the movie directly on web or display the movie from a slide viewer,
e.g. Microsoft PowerPoint.
The Mouse acts as following on the molecular system in DISPLAY mode:
left button : rotate
middle button : translate for single structure, pop up menu for multiple structures
right button : zoom
4. Integreted With Garaphic User Interface
The program has been integrated into MOIL GUI. Users can set all parameters through GUI
instead edit each instruction file. The instruction file is saved automatically.
Please view "MOIL Gui Guide" (gui_guide.txt) for how to use cmoil GUI worksheet.
5. Ribbon And Secondary Structure Display
Cmoil can display a ribbon of a structure with selectable colors and changable width.
Cmoil can also display secondary structure by following definiation:
Helix: phi=[-180,0] and psi=[-170,0] for 5 continuous residues, displayed as ribbon
with default color is green;
Sheet: phi=[-180,0] and psi=[ 0,190] for 4 continuous residues, displayed as arrowed
plane with default color red;
Unknow: other, displayed as undirected curve with default color yellow.
6. Surface Display
Cmoil is integrated with surface generating program, SURF, originally written by
A. Varshney, modified by R. Gillilan in package XTM at
ftp://bridge.chess.cornell.edu/pub/XTM-src.tar.gz .
From the menu, user can select to diplay full or partial surface with special cutoff.
A surface can be colored with Charge states as following:
Hydrophobic : brown
Uncharged Polar : green
Positively Charged Polar: red
Negatively Charged Polar: blue
~
~ Filename : cmoil.prog
~ History: Date Author Description
~ 05-30-2002 B.Wang Created
~ 03-10-2004 B.Wang Last modified
~