1. Why Grasp?
Grasp was first developed by Anthony Nicholls and Kim Sharp in
Barry Honig's laboratory in 1989, and the present version in 1992.
The impetus to develop GRASP was derived primarily from the creators
desire to visualize electrostatic potentials at the surfaces of
molecules. While there were already software programs available, such
as insight from Biosym Technologies, that could calculate
isopotential contours, these approaches were limited because they
could not capture local topology or shape, and the contours often
extend significant distances away from the molecule. Therefore, Grasp
was created to emphasize surfaces and electrostatics, and provides
the best method currently available to visualize molecular surfaces
and associated electrostatic potentials. I also believe that Grasp
provides a superior representation of atoms, bonds, and backbone
worms / ribbons than other programs such as insight, and therefore
provides the best images.
2. Using Grasp.
Atomic coordinates are the fundamental data structure from which
everything else is derived. External files in standard
crystallographic format, PDB, are used. To begin depress the
right-most mouse button and select read from the pop-up menu.
Grasp will then ask for the file name, and you can either select it
from the list of PDB files in your account or enter the file name
your self by typing it in. When PDB data for more than one molecule
is read into Grasp the different molecules are assigned a number that
correspond to the order in which the data was read. The molecule
number is used to identify each molecule during all subsequent
processes. For simple processes such as assigning colors and
building molecular surfaces there is no need to create formal subsets
of molecules. If however, you wish to move molecules relative to each
other, you must frst create a formal subset of the molecule(s) that
will be moved, and then set the dials to the subset. We will first
cover how to represent and color molecules by atoms, surfaces and
backbones, then we will cover subsetting and moving molecules, and
finally how to write files so that you can make images and save
models.
3. Representations of molecules (and coloring them).
ATOMS:
The standard method to represent atoms is as spheres of given
radius, referred to as CPK. Atoms can be assigned discrete colors,
and Grasp supports 99 independent, indexed colors. To color atoms you
must type in a command line that deEnes the molecule, residue(s), and
color. If only one molecule is present, or if you wish to assign the
same color to the same residues in all molecules, the molecule number
need not be defined. Colors are defined and indexed by typing
control-P, or through the colors panel, (which is accessed through
the options panel, and discussed in dtail later; see "using the
panels"). For example, to color residue 64 of molecule 2 the color
indexed as number 2, type the following command: m=2, rn=64, c=2.
The color number zero is used to hide atoms, bonds, worms, etc..
All other color numbers can be user defined. To color en entire
molecule the residues need not be specified; e.g. m=l, c=1.
The proper order for a command line is molecule, residue, color.
The residue can also be specified by side chain. For example, to
color all Iysine residues in molecule number I the color indexed as
number 5, use the command: m=1, r=lys, c=5. Grasp use the
three letter codes for all amino acids.
NOTES:
SURFACES:
A second way to represent a molecule is build a molecular surface
of the molecule. The molecular surface is deOned as the boundary of
that volume within any probe sphere of given radius (meant to
represent a water molecule) sharing no volume with the hard sphere
atoms that comprise the molecule. Building a molecular surface takes
only a few seconds, and results in a smooth tessellation of the
surface, which is colored white.
TO BUILD A MOLECULAR SURFACE:
Surfaces are constructed by going to the build sub-menu
using the right most mouse button. Then highlight and select
molecular surface. At this time you will be prompted to dehme
the molecule(s). Highlight and select all molecules if this is
what you desire. Otherwise highlight and select enter string,
and then type the molecule number(s) as m=i, j, etc.(where "i"
and "j" represent molecule numbers). You have now defined the
molecule(s), and in a few seconds the surface will be displayed. You
can now calculate and display the surface electrostatic
potential.
The first step is to read the radius / charge file
that contains Poisson-Boltzmann (PB) solver, which is a simpler
version of that used by DelPhi. To do this use the right most mouse
button and select the read sub-menu, and then select
radius/charge file. Grasp will now prompt you for the file,
and you should select let me enter B.le name, and then type in the
file name command: /usr/local/grasp/data/full.crg. Grasp will
read the file, and then you need to calculate e the electrostatic
potential of the molecule(s). To do so, select calculate from
the pop-up menu, and next select new potential map. Now you
need to again select calculate from the first-level menu. This time
select potential map via surfaces / atoms. Grasp now prompts
you for the molecule(s), and you need to select the appropriate
response: either all molecules or enter string. If you select
enter string, proceed as above, and type in the molecule number (e.g.
m=i, n, etc.). The final step is to select all atoms when
prompted, unless of course you wish to enter a subset of atoms. The
default colors for electrostatic potentials are red, white, and blue.
with red for the minimum value (typically negative), white at zero,
and blue for the maximum value (typically positive). The user can
increase or decrease the gain by toggling the levels on the bar at
the top of the screen.
COLORING SURFACES:
Surfaces can be colored by assigning colors to the appropriate
vertexes. In general surfaces are colored the same as atoms, with the
only difference being that you must specify that you wish to color a
surface. To specify that you want to color a surface, use vc=n
instead of c=n. (where "n" represents the indexed color
number). The command "c" is the default for "ac" or atom color. When
coloring all things other then atoms, "c" must be preceded with the
appropriate prefix. For example, to color the surface of molecule I
color number "4", at residues 50-59, and 80; type the command:
m=1, rn=(50,59), 80, vc=4. To define a continuous series of
residues, separate the first and last residue numbers by a comma, and
place them within parentheses.
BACKBONE WORMS / RIBBONS:
The a-carbon backbone of protein molecules can be displayed as a
worm or ribbon drawing. There are two ways to build a backbone worm.
One method is two proceed through the pop-up menus as we did to build
a molecular surface. To build the backbone worm select the build
option from the pop-up menu, and then select backbone worm
in the next menu. Finally select alpha-carbon worm, and a
worm will appear. If you are working with more than one molecule
worms will be built for all molecules. To hide worms that you do not
wish to be displayed you must color those worms color number zero.
This is done as follows: m=i, etc., wc=0. The color command is
"wc" for worm color. Accordingly, the color of the worm is chosen as
for atoms or surfaces, i.e. by using indexed colors. The portion of
the worm that corresponds to particular residues can be colored as
well, and this is done the same as for atoms and surfaces: e.g.
m=3, rn=50, wc=1 will color the backbone worm of molecule 3 at
residue 50 color number l. The second method to build a backbone worm
or ribbon is to use the objects panel (see immediately
below).
USING THE PANELS:
Many users will likely find the panel an easier way to operate in
Grasp, and they can be used for many procedures. The panels
are accessed through the first-level pop-up menu. There are
object panels, and options panels. To build, hide, display, or
alter the parameters of any object the objects panels are used. The
options panels allow you to access the color panel, where you
can create, define and index colors for coloring atoms, surfaces,
etc. Another option panel that is very useful is the rotate and
translate panel. This allows the user to adjust the rate at which
molecules are rotated and translated on the screen. This is very
useful, and I will come back to this later (see moving objects). For
now we will learn how to build a backbone worm using the panels. From
the "objects" panel click on the backbone worm button, and you
will see menu appear. At the bottom of the menu click on build a
worm, and worms will appear for all molecules. Using the upper
portion of the menu you can select the type of worm that you like,
and I recommend that you click on each button to see what the
different choices are. I prefer the "variable thickness" selection.
The parameters button in the lower right comer of this menu
allows you to adjust the worm parameters when the wormed is displayed
as "variable thickness".
BONDS:
The last conventional representation of molecules is to display
the bond arrangement. Bonds can be hidden and displayed by using both
the pop-up menus and the panels. Both of these methods will hide or
display all bonds on all molecules. To display only a subset of the
bonds, you must hide the others by setting the color to zero. The
bond color command is be, and this is done as follows: m=1, bc=0 will
hide all bonds on molecule l. You can then color bonds you wish to
view, e.g. m=1, rn=64,116,152, bc=6 will then color bonds of
residues 64,116,152, color 6, or m=1, r=gly, bc=2 will color
all glycine bonds color number 2. The bonds of a molecule are only
visible in the absence of displayed atoms and surfaces. The bonds can
be displayed as lines, sticks, or rods, and the thickness of
the rods can be set by the user. These parameters are most easily
adjusted by clicking on the bonds button on the objects panel.
This will give you a menu where you can select from these options
(lines, sticks, and rods).
Hiding and Displaying Objects: Using the panels you can also
hide or display atoms, bonds, surfaces, worms, etc. The button to the
right of each panel button will hide or display that object. This
will hide atoms, bonds, etc., for all molecules. If you wish to hide
only some molecules you must do that by setting the color to
zero.
DISPLAYING DNA OBJECTS:
DNA objects can be displayed in the same way as protein
molecules, i.e. as atoms, surfaces, backbone ribbon, and bonds. The
only difference between DNA and proteins is in building DNA
backbone ribbons. The only method I know of to build a DNA ribbon
is by the panels route. To do this click on the DNA objects
button, and then select build backbone. Backbone ribbons
will appear for all DNA strands up to four. In an unexplainable
quirk, the limit for DNA backbones has been set to four, and this can
not be changed without re-writing the code. I also know of no way to
change the default coloring for DNA backbones. You can however select
a tube or ribbon representation using the buttons on the menu. You
can also select different base and sugar representations, or choose
to hide the sugars and bases. This part of the program was written by
a graduate student, and unfortunately contains a few glitches as I
mentioned above.
4. Subsetting and moving objects.
Objects are moved by selecting the molecule(s) that you wish to
move, and then executing rotations and translations with the mouse.
If you are working with only a single molecule, or alternatively you
want to move all molecules together, there is no need to create
formal subsets, and to select molecules. If however you have multiple
molecules, and you wish to move one or more of them relative to the
others, formal subsets that contain the molecules to be moved must be
created.
CREATING FORMAL SUBSETS:
Formal subsets must be created through the pop-up menus. First,
select formal subsets from the first-level menu, and then
select create a formal subset. Grasp will then prompt you to
select the molecules you wish to make subsets for. If you wish to
make each molecule its own individual subset (and hence able to move
each molecule by itself), select make all molecules subsets.
Otherwise, select enter string, and then type in the
molecule number you want to subset. After making this choice Grasp
will require you name the subset, and will offer you a default name.
If the subset contains only a single molecule the default name will
be m(i), where "i" is the molecule number, I usually use these
names. If I selected enter string, and placed more than one
molecule in the subset I usually select enter different name,
and then type in a short name that identifies the subset.
FIXING THE DIALS TO A SUBSET / WORLD:
After creating a subset, the dials are automatically fixed to
that subset. To return the dials to the world, or set them to a
different subset, go to the formal subsets selection on the
pop-up menu. Then select either set dials to world or set dials to
a subset. If you select "set dials to a subset", Grasp will give
you a pop-up menu from which you make the selection.
MOVING OBJECTS:
The diagram below illustrates how to move objects with the
mouse. At first it is a bit cumbersome, but with practice I think you
will find it adequate. You can adjust the rate at which molecules
move. This is done by using the rotate and translate panel,
which is found in the options panel. Increasing the values in
the rotate and translate boxes at the bottom of this menu will
increase the speed at which molecules move. Values of 0.1 for
translation, and 1.0 for rotation are reasonable values for gross
movement of objects.
5. Saving models and making images (writing
files)
Models are saved by writing a PDB file of the coordinates the
molecules. Coordinates can be written for all molecules or a only
subset if you wish. If you have only one molecule. or if you did
not create formal subsets. you simply write a PDB file using the
write command in the first-level pop-up menu. Grasp will
prompt you for a name which needs to end ".pdb" (e.g. model.pdb), and
will ask you to either select "all molecules" or to define which
molecules are to be written. I always select from the subsequent
prompts absolute centering, and then radius and charge
data. It takes only a few seconds to write the file. If you
have created formal subsets, then you must first fix the rotation
of each subset. This is done through the formal subsets menu.
Select from this menu fix rotation of subset, and be sure to
do this for each subset. If you fail to fix the rotation of a subset
the coordinates will be written, but it will arranged arbitrarily
relative to other molecules.
Images are made in Grasp by writing a RGB snapshot file of the
image on the screen. This is done by using the write command
in the first-level pop-up menu. From the write sub-menu select RGB
snapshot file. Grasp will then prompt you to enter in a name for
the file, and after you do this it will write the fle. After
converting your RGB file to a JPEG or TIFF file, in a program such as
XV, it can be opened in PhotoShop (available on the SGI "loop") and
imaged.
6. Summary / important reminders.
ATOMS c= BONDS bc= WORMS wc= SURFACES VC=
(10) Below is a list of commands to subset residue
types (e.g. hydrophobic residues, polar residues etc.) HYDROPHOBIC
POLAR CHARGED GLYCINE
HYDROPHOBIC r=hyd (A,V,L,I.M,F,P) POLAR r=pol (S,T,Y,H,C,N,Q,W) CHARGED r=crg (K,R,E,D) GLYCINE r=gly I.I for specific amino acids use the three letter
code
e.g. r=hyd, c=2
colors all hydrophobic residues the color indexed as number 2