Modelling Series
Learning about doing measurements on molecules and docking them together.
Author:
Susan Jean Johns
Information on how far apart atoms or portions of a molecule are from one another is determined by doing measurements on the molecule(s) of interest. This process can be as simple as determining the actual distance between two points (i.e., atoms), or as complex as attempting to get dimensions on a globular protein.
Determining the distance between two atoms is usually a feature of every modelling package. The user selects this option and then picks the atoms of interest to have the distances determined for. Some packages expand this slightly to allow the user to find all atoms within a given distance from a desired point. How these neighbors are represented and what you can do with determined information varies, but can be very useful.
Measurements can be performed on other items as well, such as bond and dihedral angles. Some software allows for the determining of the angles between selected sets of atoms in a plane and another selected set of atoms in a different plane. This is handy when working with aromatic group interactions.
Molecules have size and mass. This is a concept that is sometimes lost when stick models are used to represent them. When their size is taken into account, the structures being worked with are somewhat larger than expected. Stick models can give false impressions about the amount of space that a molecule occupies or the space that exists between molecules that have been docked to one another because the atomic radii of the atoms have not been represented in any manner.
To determine the measurements dependent on the consideration of actual atomic radii, another form of molecular representation must be used. Such measurements are usually performed on Van der Waals displays of the molecule. Working in three dimensions is not the same as with two, particularly on a terminal that simultaneously shows only two of the three dimensions that you are concerned with. Any external caliper should not create optical illusions that can distort your perceptions of the structure.
A simple visual docking of two molecules is not as simple as it would appear to be due to the problems of working in three dimensions on a display device that is only good at showing two. Most docking procedures begin with the user bringing the molecules to be docked into close proximity with one another.
With MacroModel, docking can proceed along any of three paths, a simplex search, a docking through minimization or a dock procedure. Let's explore each of these techniques to find the best solution for any given docking attempt. Each uses a slightly different approach to the problem and can produce different results.
Week 8 Exercise
This exercise will acquaint you with doing molecular measurements, the various methods of docking molecules together. The bulk of your work this week will done on model1.
1) Log into ribozyme.
Pressing any key changes the terminal from screen saver mode to active. From the Launcher window select the RIBOZYME icon and press the mouse button twice. Once you have logged in, create a subdirectory for this week's work and copy cover the necessary files.
% mkdir week8 % cd week8 % cp $GRAD_DIR/week8m/*.* .
Since you will be running MacroModel sessions on model1, log off of ribozyme and use the Launcher window to start a session on that machine.
2) Log into model1.
From the Launcher window select the MODEL1 icon and press any key. Successful connection to model1 is denoted by the appearance of a model1 information line and a Username: prompt.
3) Collection of necessary data
There are various pieces of data necessary to carry out this exercise. Do a directory listing to insure that you still have the following files in your account. The required files are the simple molecules you entered for doing surface area and volume studies last week.
Required data files are:
mol1.dat mol2.dat mol3.dat
Use MacroModel to determine the distances, and both bond and dihedral angles for a number of sites in the molecules that were created for the surface and volume studies last week.
Activate MacroModel by typing mmv30.
Once in the program, respond to the first question by pressing RETURN. Then answer the question about what terminal you are using by entering 7 for Versa Term Pro .
Since the molecules to be used are all very small, read all three molecules into the same screen. Use READ, give the filename of molecule 1, press RETURN for the structure number, READ, give the filename of molecule 2, n to keep the existing structure on the screen, READ, the filename of molecule 3, and n to keep the other two structures on the screen.
Determine the following measurements from the three molecules on the screen: 1) the distance between the oxygen of the hydroxyl group and the last carbon in the longest chain of each molecule, 2) the bond angle of the oxygen and two carbon atoms up from it, 3) the dihedral angle of the oxygen and three carbon atoms up from it, or in the case of molecule 3, two carbon atoms and a hydrogen. Diagrams of the desired measurements to be made are shown on the next page along with spaces to record the determined values. The points of interest are denoted by an asterisk (*).
measurement 1 (distance between atoms - 2 points)
CH3 CH3
* * * | * * | *
CH3-CH2-CH2-CH2-OH CH3-CH2-CH-OH CH3-C-OH
|
CH3
molecule 1 molecule 2 molecule 3
To do these determinations, get into the ANALYZ portion of the program. Select ADist to determine atom distances. Then move the cursor to first one atom, press the mouse button, move the cursor to the second atom of interest and press the mouse button again. The distance between the two atoms will be displayed and a purple dashed line will be drawn between the two selected atoms. Do this for all three molecules and record the values determined below.
mol1: ______________ mol2: _______________ mol3: _______________
measurement 2 (bond angle - three points)
CH3 CH3
* * * * | * * | *
CH3-CH2-CH2-CH2-OH CH3-CH2-CH-OH CH3-C*-OH
* |
CH3
molecule 1 molecule 2 molecule 3
For bond angle determinations, select BAngl. The program will prompt you for the three atoms of interest. Use the cursor to select them. Make sure that they are connected to one another. After the three atoms have been selected, a dashed purple line will be drawn to indicate the angle selected and the size of that angle will be displayed. Do this for all three molecules and record the values found below.
mol1: ______________ mol2: _______________ mol3: _______________
measurement 3 (dihedral angle - 4 points)
CH3 CH3
* * * * * | * * * | *
CH3-CH2-CH2-CH2-OH CH3-CH2-CH-OH H-CH2-C*-OH
* * |
CH3
molecule 1 molecule 2 molecule 3
Selection of DAngl allows for the determination of dihedral angles. The program will prompt you to select four atoms of interest. Use the cursor for this task. Again the selected atoms need to connected to one another. Once selected, a purple dashed line will be drawn to indicate the angle the value is for, and that value will be displayed. Do this for the three molecules, recording the determined values below.
mol1: ______________ mol2: _______________ mol3: _______________
4) Measuring distances from Van Der Waals structures
Before you start this section copy over the demo log file with the logical name, measure, that you will need.
$ copy measure *.*
Watch the demo that is contained in measure.log. This is a section of the modelling tour you saw at the beginning of the semester. In this portion of the tour, you will see four 60-carbon fullerenes drawn on the screen along with two different colored sets of long chains of a hydrocarbon molecules. The fullerene molecules shown are actually spheres. When displayed on the terminals they are distorted in the y direction. Van der Waals surfaces will be drawn around the fullerene structures. These will appear to not quite touch the colored hydrocarbon chains. This is due to the presence of the hydrocarbon chains. After all of the surfaces have been drawn, an atom distance will be done between each of the two sets of colored hydrocarbon chains. This distance will be reported on the screen as about 4.1 angstroms. The demo stops at this point and awaits your actions.
Activate MacroModel by typing mmv30.
Once in the program, respond to the first question with measure.log and respond to the second question with n. The tour will start and stop when the picture described above is completed.
What you will see on the screen is an example of the use of a molecular ruler to determine distances for Van der Waals surface displayed models. This picture was created in the following manner. First, a pair of 60-carbon fullerene molecules were read into the program. Van der Waals surfaces were generated around each of them. Then one of the structures was visually moved next to the second one so that their VDW (Van der Waals) surfaces almost touched. The orientation of the molecules was changed to have one molecule above the other via the global rotation buttons and then a file of the structures was created.
This newly created file was then read in and VDW surfaces were generated around the newly read in molecules. The orientation of the molecules was adjusted until each molecule was almost touching two other fullerene molecules. This is probably closer than such a structure would exist in nature unless the system was subjected to extreme pressure. The results were again saved.
At this point, another file was read in that contained one of the molecular ruler structures. The original file differs from what is currently displayed on the screen: there are two long chain molecules which have a dummy bond connecting them so that both chains can be moved as a single unit.
This structure was then positioned so that one of its long chains just touched the outside edge of one of the fullerene molecules' VDW surfaces in the middle of the screen through the INPUT's ORIENT and Trans buttons. The bond was then deleted between the two portions of the ruler structure, and the chain that was not in contact with a fullerene surface was moved via ORIENT, Mol, selection of the desired chain, and the Trans button to just touch the fullerene across from the first one. A similar procedure was used to position the second molecular ruler.
With the two rulers in position it is possible to determine the size of the gap between the four fullerene molecules, taking into account the actual size and shape of the atoms involved. This is possible because of the nature of the molecular ruler. Its two chains are parallel and aligned with one another. Therefore, by moving the second chain in only one direction via ORIENT's Trans button, the parallel and aligned confirmation is maintained and accurate measurements are possible.
To gain experience with this procedure, determine the x, and y dimensions of one of the simple molecules used in the previous section, and then the radius of the 60-carbon fullerene molecule with your own ruler following these instructions after the demo is finished.
a) Create your own molecular ruler.
First, get into the INPUT mode of the program. Delete the current structures on the screen by selecting the DELT button and pressing the mouse button three times. Respond to the question about deleting the current structures with y.
Select GROW, then CH4 and press the mouse button enough times to generate a hydrocarbon chain with between 10 and 15 carbon atoms in it. Select GROW again to turn off the option. Use the Rot Z button and move the structure by -5 degree increments to get it orientated straight up and down on the screen. Use the Rot Y button to rotate the structure 90 degrees. Save this structure to a file. Read in the saved file onto the screen, saving the original structure. The two structures on the screen will be parallel and aligned with one another. Create a dummy bond between two carbons at one end of the structure by using the Draw button and moving the cursor to the desired locations. Now get into the ANALYZ mode of the program and color your creation some color other than green, using DISPLA, Mono and entering a color. Write a file of your results called rule.
b) Measure a small molecule.
Read in one of the small molecules. Keep your ruler on the screen. Generate a VDW surface around the small molecule by selecting SURFAC, using Mol to choose your desired small molecule, VDW, Rad, responding with .85 to the radius size, Dens (a level of between 2 and 4 would be best), Start and then respond with w to work with just the chosen molecule.
Move to the INPUT section of the program and select the ORIENT button. Use Mol to select the ruler molecule, and then Rot, enter z, 90, * and press RETURN. This set of actions has rotated your ruler complex to a horizontal configuration. Now use Trans, x and enter distances on the x axis that will move the ruler complex so that its middle is over the molecule with the VDW surface. Enter * when you are satisfied with the location.
Now work along the y axis to get the top portion of the ruler to just touch the top of the VDW generated surface. In this case you want to move down the screen, so enter negative values. To do this enter y and then give y distances until the top portion of the ruler complex is where you want it. At that point enter * again and then press RETURN to get out of this mode of operation.
To get the second point for your measurement, it is necessary to break the dummy bond holding both portions of your ruler together. Press DELT once, move the cursor over to the middle of the dummy bond and press the mouse button. The lower section of the ruler is now free to move on its own.
Use Mol to select the lower portion of the ruler to work with. Then use Trans, y and give y distance values until the lower portion of the ruler is where you want it, just touching the outer edge of the VDW generated surface at the bottom of the molecule. Enter * to work in the y direction, and press RETURN to exit the option.
Select ANALYZ, ADist and then two points on the carbon chains of the ruler that are aligned with one another to determine the y dimension of this molecule. Record this value below.
y dimension __________________________________________________________
At this point remove your ruler parts and start the process over again with a new ruler to determine the x dimension of the molecule. Use the information given above as a guide in this process. Record your results below.
x dimension __________________________________________________________
c) Measure a large molecule.
Clear the screen of previous efforts. Read in the 60-member fullerene. Its logical name is sball. Now generate a VDW surface around the structure. Select ANALYZ, SURFAC, VDW and Start. Read in your ruler file, keeping the fullerene data. Read it in a second time to determine the radius in two directions, since the distortion is so bad on the screen.
Move your rulers around so that you can determine the radius of this molecule in the x and y directions. When you have your rulers positioned, determine the actual distances between them. Save the results in a file called ball. Record the radius value below.
average radius ________________________________________________________
Read in the data file with the logical name cals. This file shows a close up of the top section of a calmodulin molecule. The two calciums atoms in this portion of the structure are represented by the two aqua Z's shown on the screen. We are interested in determining the distances between each of the two calcium atoms and their nearest neighbors. Use the Clip button to zero in on the portion of the screen you want to look at. Select ANALYZ, GEOMTR, Nghbr. The screen will prompt you with Enter radius in angstroms(5): to get you to enter the distance you want to try first. The next prompt Select an atom allows you to move the cursor over to the atom of interest and press the mouse button to start the analysis process. A successful hit will show a dashed purple line going from the selected atom to any atom within the distance given.
Start with 2.2 and go up in .1 angstrom intervals until you reach the point where the calcium atom is no longer being connected to only oxygen atoms. After each new hit select the NRES button, move the cursor over to the atom that just had a dashed line drawn to it and find out what residue in the sequence it is from. Keep a record of your finds below and on the next page.
____________________________________________________________________
____________________________________________________________________
____________________________________________________________________
____________________________________________________________________
____________________________________________________________________
6) Docking molecules
Read in the data file that has been given the logical name, dock_start. Clear the screen of your previous efforts. Displayed before you will be two molecules. One is ethanol and the other a molecule with two groups capable of holding a charge.
One of the various methods of docking a molecule uses a simplex search. This can be done on the data shown before you in the following manner. Select INPUT and ORIENT to get to the proper section of the program to do this procedure. Then select Mol and use the cursor to choose ethanol to work with. Next select EMon and a graph will appear on the far left-hand side of the screen. Select the T/R button and respond to the prompt with s for search. The program will then go (in real time) move ethanol to a lowest energy position with respect to the other molecule, giving energy values as it goes.
Now move over to the ENERGY portion of the program, select the MM2 button and then the ECalc button. An energy value will be determined for the structure on the screen. Record this below on the line for the simplex value. Save this structure in a file called dock1.
Read in the dock_start file again, clearing off your previous results. This time start a regular minimization of the data by selecting Start and let it proceed through 200 iterations before stopping the process. Record the energy value below on the minimization line. Save this structure to a file called dock2.
Read in the dock_start file again, cleaning off the screen. Select the Dock button and use the cursor to select the ethanol as the molecule to be docked. To begin the process, select Start. In the docking mode, you are prompted every 5 iterations to see if you want to continue or not. Go through 60 iterations of this process. Record the energy below on the docking line and then save the data to a file called dock3.
simplex value _________________________________________________________
minimization value ____________________________________________________
docking value _________________________________________________________
Now call up the dock_start data and the three files that you created in the order in which you created them. Have all four files displayed on the same screen. Move over to the ANALZY portion of the program and select the HBOND button. Notice that in each set of molecules one hydrogen bond was produced. Also notice that the different processes produced movement of ethanol in different directions and had other impacts on the involved molecules. Write this composite data to a file called group.
7) Docking larger molecules
There are times when you want to attempt to dock larger molecules than were used in the previous section. As the size of the molecules increases the ability of the MacroModel to carry out all three types of docking decreases. In this section you will be attempting to dock a carbohydrate substrate into the lysozyme binding site. With this size of molecules only the simplex docking procedure will still work.
The molecules are large enough that showing the atom labels makes the screen clutter and confusing, therefore select the A LAB button and change its color from green (active) to white (inactive). Read in the file docks, clearing off the working window of any previous molecules. The resulting image on the screen is that of lysozyme (on the left) and the substrate (on the right).
Select INPUT, ORIENT, Mol and select any atom of the substrate structure with the cursor. After the beep, select Trans. Move the substrate first in the y directions by entering: y<rtn>, and then 8<rtn>. The substrate will disappear and be redrawn on the screen just off the tip of the lysozyme molecule. Then enter *<rtn> to complete the movement of the molecule in the y direction. Now move the substrate structure in the x direction to nestle it in the binding pocket by entering: x<rtn> and then -12<rtn>. Once the substrate is in the pocket enter *<rtn> and press the RETURN key to exit the translation operating mode.
Select EMon. A small grid will appear in the left side of the screen. Select T/R, and respond with s for search. The program will start to position the substrate in the pocket. Repeat this process. More lines will be drawn on the graph. This time a yellow one will appear. Use the cursor to select this line off the graph and press the mouse button. The substrate will be redrawn in the location of this energy value (the lowest of the two search procedures run).
Select EMon again, this time inactivating the button. Now use the Clip button to zero in on the pocket region of the image. Put the cursor in the small blank area in the middle of the lysozyme molecule and press the mouse button. Then move the cursor off to right beyond the substrate to a position on the screen which would include the upper reaches of the binding pocket.
To draw a Van der Waals surfaces on the data on the screen, proceed by first putting the VDW surface on the substrate molecule and then the displayed portion of lysozyme. This is done by selecting ANALYZ, SURFAC, VDW, RAD, responding with .85<rtn> to the surface radius prompt. Toggle through the Dens values to get to Hi density level 3. Then select Mol and use the cursor to select an atom of the substrate molecule. Pick Mono and respond with p<rtn> for purple and w<rtn> for working set. Select Start and respond with w<rtn> for working set. The surface area values are displayed and then purple dots are drawn around the substrate molecule.
Create the VDW surface around the lysozyme molecule next. Pick Mol selecting any atom in the lysozyme molecule. Select Mono and respond with g<rtn> for green and w<rtn> for working set. Pick Start and respond with w<rtn> for the working set. This time green dots are drawn around most of the lysozyme molecule exposed on the screen.
Look closely at this image. Does the docked substrate appear to be in the ideal location? Do any of the dotted surfaces intersect? How would you go about determining if docked molecule is in the best location or not? Save the image on the screen by writing the data to a file called dock. Respond to the prompt Save displayed fragment only? (N,Y): with y. Exit the MacroModel program.
8) Convert and ftp over data to ribozyme.
Convert your dock file to a PDB formatted one by running the dock file through the mmodpdb program. Use the example given below as your guide.
$ mmodpdb THIS PROGRAM READS V1.5-2.0 MACROMODEL STRUCTURE FILES AND PRODUCES FORMATTED PDB STYLE OUTPUT FILES Enter MacroModel input filename: dock.dat <rtn> Enter .PDB output filename: dock.pdb <rtn> Charge file (.CHG) not found, charges set to 0.0 [structure name if any] Enter MacroModel input filename: <rtn> FORTRAN STOP
With your data file converted into a PDB formatted file, modify the results to allow for the displaying of secondary structure information with Molscript. This means that you need to go through the converted data file and trim out those residue fragments that are not complete enough to determine which atom in the set is the alpha carbon. Change the coordinate lines you have determined to be alpha carbon lines from C0X lines to be CAspace. Usually these lines have either a C01 or a C02 in them and are followed by another C0 and O0 line. The chain identifier changes from X to S. When this happens, change the residue names of the S chain atoms to UNK. Delete all the CONECT lines.
Closely examine the results of your editing to see what parts of the lysozyme chain are left. Check to see if the chain fragments are at least two residues long. It has to be that long for Molscript to handle the data. Record the remaining fragment sections below.
fragments: ___________________________________________________________
$ ftp ribozyme.vadms.wsu.edu model1.vadms.wsu.edu MultiNet FTP user process 3.4(111) Connection opened (Assuming 8-bit connections) <ribozyme.vadms.wsu.edu FTP server ready. RIBOZYME.VADMS.WSU.EDU>l bcsxx<rtn> <Password required for prcadams. Password:(enter your own password<rtn>) <User prcadams logged in. RIBOZYME.VADMS.WSU.EDU>cd week8<rtn> <CWD command successful. RIBOZYME.VADMS.WSU.EDU> type ascii<rtn> Type: ASCII (Non-Print), Structure: File, Mode: Stream RIBOZYME.VADMS.WSU.EDU>put dock.pdb<rtn> To remote file:<rtn> <Opening ASCII mode data connection for 'pos.pdb'. <Transfer complete. RIBOZYME.VADMS.WSU.EDU>quit<rtn> <Goodbye.
You are finished on model1 so log out off your account and get back into your ribozyme account. This time make contact with ribozyme through the X RIBOZYME icon in the Launcher window. Once there, move over to the week8 subdirectory location.
9) Creating an image from the dock file data.
One of the files moved over to this location at the beginning of the exercise is a control input file for the dock image, called dock.in. Because of the variations that will occur in the clipping process, it will be necessary to check this file to see if it matches the actually fragments you have. Use the feature data below to help in the secondary structure assignments.
F;1-3,38-40/Region: beta sheet F;5-15/Region: helix (right hand alpha) F;25-35/Region: helix (right hand alpha) F;42-46,50-54,57-60/Region: beta sheet F;80-84/Region: helix (right hand 3-10) F;89-96/Region: helix (right hand alpha) % pico dock.in
Once you have the dock.in file in shape create a postscript image of the dock results.
% molscript <dock.in> (your lastname)-dock.ps
This time instead of using the printer to see what the resulting postscript file looks like, use the program ghostscript (gs). Ghostscript is an interpreter/previewer for looking at postscript files on an xterm. The program has many other display options than what you will be using today.
% gs (your lastname)-dock.ps
The introduction to the program is displayed on the screen and then a second window appears on the screen in which the actual image is drawn. If you are using a color monitor, the image displayed will be in color if so defined by the postscript file. The actual colors shown are dependent on the display device. The color produced on a terminal screen will be slightly different from than that of a color print produced from the same data file.
After you are finished looking at the image on the screen you need to get back to the xterm window to get out of the program. You can do this in one of two ways. By selecting a portion of this window if it is still exposed behind the displayed image with your mouse and clicking the mouse button to bring it up in front of the image window. Or you can select ribozyme.vadms.wsu.edu from the Window menu of the MacX control bar at the top of the screen.
Back in the xterm window, press the RETURN key to get to a GS> prompt. To exit the program enter quit.
10) Creating a Molscript control file from Rasmol.
RasMol is a program that runs on a number of different platforms for the visualizing molecules. It can run on Macs, PC and Unix platforms. To activate the program and use it to look at the calmodulin molecule you used before for determining distance information enter the command line on the next page.
% rasmol 3cln.pdb
Another window appears on the screen. In this window a wire frame structure of the molecule is drawn. To change the image to something more like a secondary structure representations you are familiar with select Cartoons option from the Display menu of the program's control selections at the top of the window. A standard helix and sheet cartoon of calmodulin is displayed in the window. Now select the Structure option from the Colours menu of the control selections. The image in the window is colored as follows: helixes are pink, strands yellow, turns powder blue and white for random.
There is an option in this program that allows a user to create a Molscript input control file for the data displayed in the window. This option reads the data lines for the protein portion(s) of the data shown on the screen from a PDB file and generates corresponding secondary structure display language. To do this, do the following steps.
Get back to the control window of the RasMol program. This is done by selecting a portion of this window if it is still exposed behind the displayed image with your mouse and clicking the mouse button to bring it up in front of the image window, or by selecting ribozyme.vadms.wsu.edu from the Window menu of the MacX menu bar at the top of the screen.
At the RasMol> prompt enter the following command line.
RasMol> write molscript 3clnx.in <rtn>
When the prompt returns enter quit and press the RETURN key. The display window should disappear and the normal ribozyme prompt return.
Use pico to examine the produced file. For some reason the RasMol generated file puts in a window statement to make the image smaller than it should be, therefore remove the window line. The calmodulin file actually contains coordinate data for residues 5 from 147 of the sequence that is given in the SEQRES section. Any control lines for residues 1 through 4 and beyond 147 aren't supported by the actual data. Remove any lines for data not contained in the original PDB file.
Organize the data via secondary structure groupings: helix, coil (random), turn, and sheet. Change the turn residue lines into turn from x to y lines. In this example x is the starting point of the turn and y is the ending residue. Modify the coil lines to take into account the turn assignments. You will need to add more of these lines to fill in the gaps before and after the turn locations.
turn from 20 to 22; coil from 19 to 20;
The RasMol file makes no attempt to color the structure, you need to supply those lines yourself. Use set planecolour lines to do this. Color the helixes red, coils white, turns yellow and sheets cyan.
set planecolour red;
A RasMol generated file also makes no attempt to deal with non protein coordinate lines. One of the important features of this structure is the location of its calcium ions. Put in the following three lines to color, set the atom radius and draw the ions.
set atomcolour in type CA purple; set atomradius in type CA 3.0; ball-and-stick in type CA;
Likewise the RasMol file doesn't put in any type of a label. Enter the following lines to put in an appropriate label.
set depthcue 0.0, labelsize 30.0; label 5.0 -5.0 0.0 "Calmodulin*";
Run Molscript on your transformed input control file.
% molscript <3clnx.in> (your lastname)-cln.ps
Use ghostscript to visualize your results. Use the instructions contained in section 9 to help you use the program.
% gs (your lastname)-cln.ps
Check to make sure that your image is a completely connected one. If it isn't, go back and make the necessary adjustments in the control file to correct the situation and go through the process again until it produces the described results.
11) Finishing up
Rename the report form to have your last name, and then using the pico editor fill it out Send it to the teacher account. When that is completed, rcp over the two image files you created to teacher as well.
% mv week8m.week8m (your lastname).week8m % pico (your lastname).week8m % rcp (your lastname).week8m teacher@ribozyme:receive % rcp (your lastname)-dock.ps teacher@ribozyme:receive % rcp (your lastname)-cln.ps teacher@ribozyme:receive
This concludes your computing session for this week. Log off of ribozyme, get out of the emulator and back to the Launcher window screen.
Per J. Kraulis, "MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures", Journal of Applied Crystallography (1991) vol 24, pp 946-950.