Covered in this exercise: (1) Unix shell commands mkdir, cd, pwd, ls, more, and rm.
(2) MidasPlus commands color, conic, chain, ribbonjr, display, Ctrl-p, Ctrl-n, label, open, window, vdw, stereo, surface, pdbrun, midaspush, midaspop, reset, close, move, set independent, match, save, and stop.
This exercise has you attempt to dock an inhibitor into the active site
of a protein, while learning basic MidasPlus commands.
Note: Descriptions are of OpenGL MidasPlus running on Silicon Graphics workstations,
system 5.3 or higher. In the GL version, the control panel will look somewhat
different (active models are shown by highlighted numbers but their filenames
are not shown, and to reach the sliders you must click on "Sliders"); other
behavior should be similar.
(1) Log in.
(2) Make a directory to work in. Use the command:
mkdir directory_name_of_your_choice
Note that your directory name cannot contain spaces.
(3) Go into that directory using the command
cd directory_name_of_your_choice
and display the MidasPlus demo file that has been prepared. Give the following command:
midas -f /usr/local/midas/tutorials/cgl/ex1/protein.pdb
The "ex1" stands for exercise number one; make sure you don't type a letter
"l" instead of the number "1"! You are now within MidasPlus. You should
see the molecule on your screen; it is the HIV-1 protease. The large cavity
in the middle is the active site. The MidasPlus control panel is in the right lower part of the screen. Near the bottom of the control
panel is a highlighted line (may appear black):
0:/usr/local/midas/tutorials/cgl
(In the GL version, there will just be a highlighted "0") This means that
model 0 is active and contains the molecule; normally, the whole name of
the file would show, but in this case it is too long. The middle of the
control panel contains a side view representation of the molecule. Your
eye position is shown as a small square, and the two vertical lines are
the clipping planes. Try rotating the molecule, getting used to the trackball
(virtual sphere) method. Using the middle mouse button, you can translate the molecule. The left mouse button allows you to rotate around the X and Y axes when the cursor is inside the
circle and rotate around the Z axis when outside the circle.
In the side view area of the control panel, you can make the molecule larger
or smaller by moving your eye position (the small square) with the left mouse button. Similarly, you can control the "slice" of molecule that is visible by moving the vertical lines.
Use the following MidasPlus commands to alter the appearance of your protein.
To enter commands, move the cursor out of the control panel to any other part of the screen. The words to type are shown to the right
of the word "command" below.
command: color cyan
this colors everything cyan.
command: color red @o
where @ means atom; this colors all the atoms named "o" or "O" red.
command: color yellow @s=
where = is a wild card; this colors all the atoms whose names start with
"s" or "S" yellow.
command: conic
this makes a space-filling model. When the image is fully drawn, clicking
the left mouse button will return you to the MidasPlus screen.
command: chain @ca,c,o,n
this displays only the backbone atoms of the protein, making the secondary
structure easier to see.
command: ribbonjr -a
this makes a ribbon model; the backbone atoms "ca" and "o" must be displayed
for this com mand to work. The -a option instructs MidasPlus to only show
the backbone in the ribbon drawing even if the side chains are displayed
when the command is typed. When the image is fully drawn, clicking the left
mouse button will return you to the MidasPlus screen.
command: display :30-40
where : means residue; this causes all the atoms in residues 30 to 40 to
be displayed. If only the backbone was displayed before, the sidechains
will now appear.
command: color yellow :1-99
command: color cyan :101-199
This protein is a dimer; you just colored one monomer (residues 1 to 99)
yellow and the other (residues 101 to 199) cyan. Now repeat the ribbonjr command (above); instead of retyping, you can use
command: Ctrl-p
(holding the "Ctrl" key down, press the "p" key) Repeat to keep accessing
the previous com mand. When you have gone far back enough for the ribbonjr command to reappear in the com mand line, hit return. See Appendix 3 in
the MidasPlus manual for a listing of similar shortcuts. Remember that when
the image is fully drawn, clicking the left mouse button will return you
to the MidasPlus screen.
command: Ctrl-n
will scroll forward through the commands. An easy way to remember these
shortcuts is that "p" stands for "previous" and "n" stands for "next."
(4) Labeling is also possible.
command: label
When no specification follows the command, the command applies to everything.
Chances are, there are too many labels on the screen now! Get rid of them.
command: ~label
In general, ~ means "un" in MidasPlus. Now label a specific atom. Type "label" and then a space,
but do not hit return...
command: label (DO NOT PRESS RETURN YET!!!)
now pick an atom by holding the Alt key down while clicking with the mouse
on the atom of interest. The cursor should look like an arrow while the
Alt key is being held down. After you have picked one or more atoms, the
names of the atoms should appear in the command line after the word "label."
You might see something like:
command: label #0:5@ca
By NOW hitting return, you can execute the command. You can also label everything
that is a certain color, for example:
command: label /color=yellow
where the /color=yellow part means "everything that is colored yellow." If you had used /color=blue instead, nothing would get labeled since nothing is blue. See section 2.1.3
in the manual for a listing of ways to specify atoms by their characteristics.
(5) Open a second model and do a mock docking experiment. A file has been
prepared, named /usr/local/midas/tutorials/cgl/ex1/moved.pdb.
command: open /usr/local/midas/tutorials/cgl/ex1/moved.pdb
Since model 0 is in use, the new structure is placed in model 1. This is
a peptide analog that inhibits the HIV-1 protease. To make it easier to
see, you can bring it to the center of the win dow:
command: window #1
where # means model number. Click once on the highlighted line for model
0 (near the bottom of the control panel) so that the line changes color.
When lines are highlighted, the correspond ing models are selected for motion.
One click unhighlights the line of text and deselects the model for motion;
another click selects the model again. Now that only model 1 is selected,
only the inhibitor should be movable. If the cursor is over the control
panel, move it out so that commands can be typed; put a VDW (van der Waals)
dot surface on the inhibitor.
command: vdw #1 Selecting and unselecting the models as needed, try to dock the inhibitor
into the active site. It may be useful to try stereo.
For Stereo:
(A) If your machine uses the Crystal Eyes stereo system: Put on the white battery operated glasses, and turn them
on with the front right button. Make sure the small box on top of the screen
is set to low, since if there is more than one system in the room, they
can interfere when set on high.
(B) If your machine uses a separate stereo screen attachment, it needs to
be attached to the front of the monitor. It is a smoky screen with a black
metal frame. If it is not attached, please enlist help, as it is very expensive and fragile. Flick the stereo
switch on the small box to the side of the monitor, and put on the lightweight
plastic stereo glasses.
In either case:
command: stereo seq
turns on the sequential stereo feature in MidasPlus. If stereo does not
seem to be working, the batteries may be low. If stereo is not working or
you prefer to continue without stereo, turn the equipment off (glasses or
separate stereo box) and discontinue the stereo feature in MidasPlus.
command: stereo off
(6) Next you can display a molecular surface, which is similar to a VDW surface
except that the crevices are smoothed out. Undisplay the VDW surface.
command: ~vdw
A molecular surface for the protein has been prepared.
command: open s 0 /usr/local/midas/tutorials/cgl/ex1/protein.surf
The surface is "there," but another command is needed to display it.
command: surface #0
displays the surface for model 0 (remember that # means model number). To
display only a por tion of the surface, you can specify particular atoms,
similar to when using the color and label commands. See section 2.1 in the
manual for a full description of atom specification options.
command: ~surface :25 z>12
this will cause all surface points more than 12 A o from residue 25 to disappear.
To undisplay the whole surface:
command: ~surface
To get the surface back, simply type: command: surface There is no need
to specify a model number, since only one model has a surface to go with
it. If you get tired or need to stop the exercise and resume it later, see (10) in this handout.
(7) Once you have found a reasonable position of the inhibitor in the active
site, try using the thickness and section features to see which surfaces
overlap in your "docked" complex. The easiest way to do this is with the
side view in the middle of the control panel. The two vertical lines are
the hither (front) and yon (back) clipping planes. Moving them with the
left mouse but ton controls what slice of the structures you are viewing.
Instead of using the side view, you can also control the slice with the
buttons on the top half of the control panel (in the GL version, you need
to click on "Sliders" to get the analogous controls). The buttons next to section control the location of the slice; holding the left mouse button down when
the cursor is over an arrow moves the slice closer to or farther away from
you, depending which arrow you choose. The double arrows result in a faster
change than the single arrows. You can see the planes move in the side view
when you do this. The buttons next to thickness control the thickness of the slice.
These controls allow you to make the display less complicated and focus
on the area of interest, in this case the match between the protein and
inhibitor surfaces.
(8) Now you can see how your docking results compare to the experimentally determined
com plex. Save your docked complex into a file named "mydock" with the following
command:
command: pdbrun cat | grep -v ^END > mydock
This saves all the currently displayed models into a file. There are several
ways of saving struc tures or their orientation matrices from within MidasPlus.
To see if a file has been created, you can bring your normal windows in
front of the MidasPlus screen with:
command: midaspush
Then, if you have or can open a window besides the one you started MidasPlus
from, you can use the following UNIX commands:
cd directory_name_of_your_choice
-to go into the directory with your MidasPlus results (the same one you
made at the beginning of this exercise, of course)
pwd
- to see what directory you are in; stands for "print working directory"
ls
- to list the files in that directory
more mydock
- to see the contents of the file a page at a time;
space bar advances the display and q quits out of more.
To get the MidasPlus screen back in front, position the cursor in the MidasPlus
part of the screen and type:
command: midaspop
The reset command can be used to restore structures to their original positions.
Close the model containing the undocked inhibitor.
command: reset
command: close 1
Then open your docked structure and the experimentally determined inhibitor
coordinates.
command: open mydock
command: open /usr/local/midas/tutorials/cgl/ex1/substrate.pdb
Notice that MidasPlus puts each opened structure in the lowest empty model
number. The origi nally opened protein structure is in model 0 (there may
be more than one "0:" line in the control panel because of the surface),
your docked structure with both protein and inhibitor is in model 1, and
the experimental inhibitor position is in model 2. To make the comparison
easier, you can change the color of one of the models, for example:
command: color red #1
to color your docked structure red. The inhibitor consists of residues 200
to 206, so to color your docked inhibitor green (for example):
command: color green #1:200-206
(9) There are actually two copies of the HIV-1 protease on the screen, the
one opened near the beginning of the exercise, and the one in the file "mydock."
It may be difficult to tell that there are two copies if they are right on top of each other. You can separate
the copies by manipulat ing models independently. Unselect models 0 and
2, that is, click on the lines near the bottom of the control panel so that
only the line for model 1 is highlighted (it may appear black). Now only
model 1, your docked structure, should be movable. All selected models (in
this case only model 1) can be moved with the mouse or with commands.
command: move x 25 1
moves all selected models 25 A o along the X axis. The "1" refers to the
number of times the movement will be carried out. You may want to scale
down the image to be able to see all of the molecules. Place the two copies
of the protein side by side by using the mouse or repeating the move command
as needed. Then click in the control panel so that all models are selected,
and try rotating. This is the default rotation behavior; the following command
will allow them to rotate independently instead.
command: set independent
Now try rotating the molecules.
command: ~set independent
restores the default rotation behavior.
To resuperimpose the two copies of the HIV-1 protease:
command: match #1 mainchain #0 mainchain
This command requires at least four atoms from one model to be matched with
four atoms from another. The word "mainchain" means the protein backbone
atoms. Now you can scale up and rotate around to see how well you did at
docking the inhibitor.
(10) Saving your work session.
command: save filename
produces several files whose names start with filename; these contain the structures that were open when you used save, as well as information about color, orientation etc. At that point you
can exit MidasPlus.
command: stop Since the session has been saved, you can start MidasPlus again right where
you left off. To do this or to just check if the session has been saved
correctly:
midas -f filename
where filename is the same name that you gave with save above. You must be in the same
direc tory as when you saved the session. Be patient, as it may take a minute
or two to start up the session, especially if it contains a large dot surface.
Before logging out, exit from MidasPlus again:
command: stop
If there are files you do not want to keep, remove them.
rm myfile
where myfile is the name of the file you want to remove. Remember that the files in
the current directory can be listed with
ls
Now you need to log out from the workstation. Just logging out of the individual
windows does not log you out of the machine. Log out completely by placing
the cursor over the background part of the screen (outside the windows),
holding down the right mouse button, and selecting the logout option. You
will then be asked to confirm whether you really want to log out - select
yes!
1/97 revised by Elaine Meng, original by Julie Newdoll UCSF Computer Graphics
Lab