Protein Explorer vs. RasMol
by Eric Martz, August 29, 2000
El objetivo perseguido al construir Protein Explorer
es permitir a las persones que se concentren en los aspectos científicos,
y no en los aspectos de programación. Chime aumenta considerablemente
la capacidad de visualización respecto as RasMol, sin embargo
la utilización al máximo de estos programas requiere conocimientos
técnicos avanzados y mucho tiempo. Esto significa que su potencialidad
se muestra inaccesible a una mayoría de gente que podría
beneficiarse de ellos. El objetivo de Protein Explorer es hacer accesible
la potencialidad de Chime a estudiantes, educadores y científicos.
Si desea más información mire en
evolucion
de los usos de Chime y propósito de Protein Explorer.
La Versión 2.0 de Protein Explorer, ofrecida
a lo largo de 2000-2001, es mucho más fácil de usar,
y mucho más potente que RasMol. Protein Explorer
requiere
Netscape (no funcionará con
Internet Explorer).
Dado que Chime solo es asequible en formato Windows y Macintosh, Protein Explorer
puede funcionar en linux, u otras plataformas, únicamente como un
Subsistema de
Windows).
The list below is not meant in any way to disparage RasMol!
Without RasMol, there would be no Protein Explorer, because it requires
Chime, which in turn is built using RasMol's source code! Protein Explorer
is possible only because of the brilliant infrastructure contributed by
Roger Sayle, the author of RasMol.
Novice Features
Advanced Features
For graphic evidence of the user-friendliness and power
of Protein Explorer, see the
snapshots.
-
Protein Explorer's first image of any molecule is
maximally
informative. RasMol's first image is wireframe, of very little use
for macromolecules.
-
Protein Explorer's first image is accompanied by FirstView,
a description of the image and how to interpret it, with additional layers
of in-depth help available through hyperlinks. RasMol provides no assistance
with interpretation. Protein Explorer includes a "Form for Recording Observations".
-
Clicking on an atom identifies clearly its element,
residue name, sequence number, and atom serial number. The latter two numbers,
in particular, aren't clearly distinguished in RasMol's one-line identification
report.
-
Protein Explorer's QuickViews menus follow the RasMol
paradigm (select, then render, then color) but have powerful options not
on RasMol's menus. In fact, RasMol has no select menu at all (except "Select
All") -- all selections must be done from commands.
The QuickViews SELECT menu includes:
-
Protein or Nucleic (with a one-click distinction between
DNA and RNA)
-
Individual chains
-
Secondary structure elements (helices, sheets)
-
Backbone, Sidechain
-
Solvent, Ligand
-
Hydrogen
-
Invert selection
-
Range of residues or any arbitrary residues (with Seq3D)
QuickViews' DISPLAY menu includes in addition to
the more useful renderings on RasMol's Display menu:
-
Trace (smoothed backbone)
-
Hbonds, SSBonds
-
Dots
-
Solvent accessible surface
-
Transparent surface
-
Cation-Pi interactions
-
Salt bridges
-
Contact surface (overview of noncovalent bonds between any
two moieties)
-
Only (hide not selected)
-
Hide selected
-
Center (all selected, or by click on atom)
QuickViews' COLOR menu includes in addition to
the more useful color schemes on RasMol's Colours menu:
-
Polarty (2, 3 or 5 colors): hydrophobic vs. polar vs. charged.
-
ACGTU scheme for reading the code from nucleotide strands.
-
A series of plain colors (red, white, etc.)
You rarely need the powerful but confusingly-organized
menus of Chime when using Protein Explorer. When you do (as for selecting
all tryptophans) detailed instructions are provided.
-
When a menu selection is made in QuickViews, context-triggered
help with color keys (for color scheme selections), and troubleshooting
information
appear automatically. RasMol offers only a reference
manual that must be invoked with commands such as "help cpk", and has no
built-in color keys in color.
-
Protein Explorer has convenience buttons to toggle
continuous slow spinning**, visibility of water or ligands, slab and stereo,
as well as buttons to zoom up or down, change between white and black background,
center any atom, or reset the initial view. RasMol has no continuous automatic
spinning capability, and no convenience buttons.
-
When a new center of rotation is specified, it also remains
in the center of the screen during zooming**. In RasMol, it often zooms
out of view.
-
Protein Explorer has a molecule information window
accessible at all times, with direct links to the PDB file header and RCSB
Structure Explorer for the PDB ID code currently loaded.
-
Protein Explorer will display the amino acid (or nucleotide)
sequences
for all chains in a readable one-letter code. Touching any residue shows
the sequence number and three-letter code. Any desired amino acids (such
as all cysteines) can be highlighted in color for easy spotting. Gaps and
insertions are shown clearly, as is the length of each chain. RasMol's
sequence display is three-letter code only, plain text, not interactive,
no help provided.
-
Protein Explorer's sequence-to-structure interface, Seq3D
highlights (and selects) any amino acids or ranges of amino acids (or nucleotides)
when they are clicked in the sequence listing.
-
When a multiple-model PDB file (NMR result) is loaded,
only the first model is shown in FirstView and QuickViews. Upon entering
QuickViews, the user is alerted that there are multiple models, and the
model count is shown in the QuickView help frame along with additional
information about how to view the other models.
-
Installation: About the same small amount of fuss in each
case, although Netscape and Chime require much more disk space than RasMol.
-
Off-line operation: Protein Explorer operates perfectly
off-line (it can be downloaded, although you don't need to download it
to use it from the web). RasMol's primary mode of operation is off-line,
although a properly configured web browser can spawn it from some hyperlinks.
Off-line use of either RasMol or Protein Explorer requires that the requisite
PDB file(s) have been downloaded. When on-line, Protein Explorer can fetch
a PDB file from any PDB mirror or other source, and get additional information
from the PDB or other sources.
-
Comparator mode allows two molecules to be compared
side by side. Any operations of Protein Explorer can be directed at either
or both molecules. RasMol has no such mode. (With either Protein Explorer
or RasMol, you can run two sessions side by side. If each session is Protein
Comparator, you can conveniently compare 4 molecules.)
-
You can load a PDB file by specifying its PDB identification
code in the hyperlink to Protein Explorer, or within Protein Explorer in
a form slot, or by browsing to a file on the local disk. RasMol supports
only the latter mode.
-
The ten most-recently loaded molecules (from local
disk or Internet) can be reloaded from a menu in Protein Explorer. No such
menu exists in RasMol.
-
Protein Explorer has over ten preference options.
The preference settings survive between sessions, and work regardless of
whether Protein Explorer is used from the web, or a downloaded copy. There
is an "expert" preference setting. RasMol has no preference settings, and
is in "expert" mode all the time.
-
In "expert" mode, when an NMR file is loaded, all
models are shown in the initial view. A special NMR Model Selection
page appears under Advanced Explorer, with the ability to play the ensemble
of models as a movie, with custom-scripted rendering and coloring if desired.
-
Advanced Explorer has detailed forms for configuring the
detection and display of cation-pi interactions and salt bridges.
These enable ligands to be included in the detection and display. This
feature has its own tutorial.
-
Advanced Explorer has a detailed form for configuring the
display of multiple solvent accessible, rolling probe Surfaces**.
Surfaces can be colored by molecular electrostatic potential or molecular
lipophilicity potential**. Among many other options available in simple
form slots, the probe radius can be changed.
-
Advanced Explorer has a detailed form for configuring the
display of Contact Surfaces. This feature has its own tutorial.
-
Advanced Explorer includes a Noncovalent Bond Finder
that allows a very detailed exploration of the noncovalent bonds between
any two moieties. This feature has its own tutorial.
-
Protein Explorer has a command-line interface that
understands nearly all* RasMol commands, plus additional Chime commands.
In RasMol, going beyond looking at the entire molecule in various renderings
and color schemes requires teletype-style commands. However, you don't
need RasMol commands for effective exploration of macromolecules in Protein
Explorer, since the menus are much more powerful.
* "Nearly all": the "save" command is disabled in Chime,
which precludes Protein Explorer from saving subsets of the atomic coordinates
(but it can save the entire PDB file), exporting GIF's or vector postscript
(but a screenshot saves a GIF from Protein Explorer), or saving scripts.
(Protein Explorer copies the script to the clipboard, so it can be pasted
into a word processor and saved.)
-
Protein Explorer understands aliases for common commands,
such as
-
s for "select"
-
spd for "set picking distance"
-
bs for "wireframe 0.15; spacefill 0.45 # ball and
stick"
-
hb for "hbonds 0.2;color hbonds white;set hbonds sidechain;"
-
m for "(cadmium,calcium,copper,iron,magnesium,manganese,zinc)"
RasMol has no alias facility. In Protein Explorer, aliases
are easily customized or added.
-
Recent commands can be recalled and edited (to save
retyping), a feature also offered by RasMol.
-
Project folder. Both Protein Explorer and RasMol can
work nicely from a project folder on the local hard disk containing PDB
files and scripts.
** These features were built into Chime by the
MDL staff that authored Chime (in some cases, at my request).