Modelling Series
Learning about determining the physical characteristics of molecules on the computer. Coloring the determined secondary structure of a molecule. Creating and using alpha carbon traces and the superpositioning of molecules.
Author:
Susan Jean Johns
A number of physical characteristics can be determined and/or displayed for molecules using modelling software. These characteristics range from various possible surface areas, to showing charges and possible hydrogen bonding patterns.
How a molecule is shaped can affect its behavior in given environments. Molecules which are highly branched present a different reactive profile than do linear ones. Molecular shape can influence such activities as retention times on separation columns and reaction rates. The determination of surface areas and enclosed volumes can provided some of the information on why a molecule behaves as it does.
Molecules which contain atoms that can carry a charge when in solution respond differently depending on where that atom is located in the structure. Those molecules which have their charged areas exposed to possible external reactive agents respond differently than ones in which such charged areas are not readily accessible. The more complex the molecule, such as a protein, the more likely the location of charged groups are to be on the surface of the molecule.
The formation of secondary structural elements in a protein is partially driven by the creation of hydrogen bonding in these structures. Determining the possible hydrogen bonding for a protein gives insight into forces which govern the protein's folding. Stripping a protein structure to its backbone and then color coding the secondary structural elements makes the folding patterns in a structure more evident.
Alpha carbon traces originated in the earliest days of x-ray structure determination of proteins. Some of the early structures were actually reported when only their alpha carbon coordinates were known. A few of these structures still exist within the PDB database.
Due to the complex nature of proteins, a simple method of visualization was sought that could convey basic information about the molecule and its secondary structure with the least amount of coordinate data. An alpha carbon trace accomplishes this. It is produced by connecting the alpha carbon coordinates in the order given by a protein's primary sequence. The resulting trace shows the general shape and secondary structural elements of the protein. Such traces could be then compared with one another to determine differences in general shapes, secondary structure patterns, and other features of interest. Traces have an advantage: structure information can be worked with using the absolute minimum of data, thereby allowing one to compare of numerous proteins at the same time.
To create such a trace, a user needs to have a file containing only the alpha carbon coordinates. This file is then converted into a file that is usable in the modelling software. With MacroModel this means that the converted file will display a collection of C's on the screen that will have to be connected in much the same manner as a child produces a connect-the-dot-picture in a coloring book, connecting each dot (C) to the next higher numbered dot (C). However, with MacroModel after the trace is produced it will no longer have the same spacing between the atoms as the non- connected data did; it will be smaller.
Therefore, to use such traces in MacroModel a whole collection must be produced to do comparisons on. The traces can be compared to one another, but not to the original data from which they were derived. All sorts of comparisons that do not depend on actual distances between points can be done.
The term superpositioning refers to the overlaying of two molecules, one upon the other, to determine the best alignment between them. It is the modelling equivalent of doing a sequence alignment. This can be done in either a rigid or a flexible mode. In the rigid mode, no adjustments to either structure is allowed. The selection of tack points controls the quality of the alignment. In the flexible mode, portions of one molecule can be changed to improve its alignment with the other. This is done by changing the angles of various selected bonds to make the best possible alignment between the tack points.
Another form of superpositioning is to overlay the primary sequence of one protein upon the coordinates of another to which it is believed to be very similar. With the limited number of folding patterns that have been found, this approach makes some sense if there is physical evidence that disulfide bonding patterns have been maintained, or the extent of similarity is very high, greater than 50%.
Week 7 Exercise
This exercise will acquaint you with the various ways of determining physical information about molecules, creating and using alpha carbon traces and the use of molecular superpositioning. Most of your work this week will be on model1.
1) Activate the computer and 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. Successful connection to ribozyme is denoted by the appearance of a ribozyme information line and a login: prompt.
Once you have logged in, create a subdirectory for this week's work and copy cover the necessary files.
% mkdir week7 % cd week7 % cp $GRAD_DIR/week7m/*.* .
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 bar select the MODEL1 icon and press the mouse button twice. 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 have the following files in your account. If not, enter the following commands to bring the missing files over. In this listing xxxx represents the PDB access code for your selected molecule.
$ dir
Required data files are:
2mlt.bdt 2mlta.nrl_3d 2mlt.pdb
1crn.bdt 1crn.nrl_3d 1crn.pdb
xxxx.bdt xxxx.nrl_3d xxxx.pdb
If any of the above files are missing, then copy the appropriate file to your account using the following command and logical assignments. The established logical names are: crambin1 (1crn.bdt), crambin2 (1crn.nrl_3d), crambin3 (1crn.pdb), melittin1 (2mlt.bdt), melittin2 (2mlta.nrl_3d), melittin3 (2mlt.pdb), selm11 (4rub.bdt), selm12 (4rubs.nrl_3d), selm13 (4rub.pdb), selm21 (6q21.bdt), selm22 (6q21.nrl_3d), selm23 (6q21.pdb), selm31 (4fgf.bdt), selm32 (4fgf.nrl_3d), selm33 (4fgf.pdb), selm41 (1sdy.bdt), selm42 (1sdya.nrl_3d), selm43 (1sdy.pdb). In the command line, yyyyy represents the desired logical name. Repeat variations on the command line given on the next page until all the necessary files are in your account.
$ copy yyyyy *.*
For the various task you will be doing this week you will need to know the secondary structure assignments. Get these assignments using the following command. In the example command line yyyyy represents the desired access code for the file. Record the assignments below.
$sea yyyyy.nrl_3d helix,sheet,turn,beta
melittin secondary structure information:
helix locations: _____________________________________________________________ sheet locations: _____________________________________________________________ turn locations: ______________________________________________________________
helix locations: _____________________________________________________________ sheet locations: _____________________________________________________________ turn locations: ______________________________________________________________
helix locations: _____________________________________________________________ sheet locations: _____________________________________________________________ turn locations: ______________________________________________________________
5) Creating an alpha carbon trace (part 1)
Create a file containing just the alpha carbon coordinates for melittin. This is done by searching the PDB coordinate file ( an ascii file) for the term " CA " and creating an output file for the data. Convert this data into a MacroModel usable file via editing and the use of bfiler.
$ sea melittin3 " CA "/out=mel.ca
Display this output file on the screen and check to see if it has the necessary MASTER and END lines. If not, use the eve to add them to the file.
$ type mel.ca $ eve mel.ca
When the file is in proper form, use the bfiler program to convert the data into a MacroModel useable data file. On the next two pages is an example of using the bfiler program. User input shown in bold type. In the example, mel.ca represents the name of the file containing the melittin CA lines.
$ bfiler
BFiler (v 0.2)
27-NOV-96 08:37:18
BFiler: SELECT A MENU ITEM FROM BELOW--
HELP=Information
TAPE=Read Brookhaven format files Brookhaven tape and
translate to MMOD format,
COPY=Copy files from Brookhaven tape to disk
without translation
DISK=Translate Brookhaven format files to MMOD files
BARE=Translate Bare Brookhaven atom table (from file(s)
disk) to MMOD format file(s)
EXIT=Exit BFiler
BFiler> disk <rtn>
BFILER-DISK:This routine attempts to translate Brookhaven
format files which are on a disk
BFILER-DISK:Continue?(y): <rtn>
Default suffix is ".BRK"
Type in the names of the files you want to process,
Hit return after each code name and
a bare "." to finish>
mel.ca <rtn>
.
Below is a list of names for files you want to translate --
Options: (1) type in corrected entry;
(2) type "i" to insert an entry,
(3) type "x" to delete entry,
(4) type "." to finish,
(5) hit return to verify entry:
mel.ca <rtn>
Go back and re-edit the filecodes?(n)> <rtn>
Looking for file mel.ca
Reading lastname.out
Reading atomic coordinates...
Typing atoms...
Creating bond entries...
BFiler: SELECT A MENU ITEM FROM BELOW--
HELP=Information
TAPE=Read Brookhaven format files Brookhaven tape and
translate to MMOD format,
COPY=Copy files from Brookhaven tape to disk
without translation
DISK=Translate Brookhaven format files to MMOD files
BARE=Translate Bare Brookhaven atom table (from file(s)
disk) to MMOD format file(s)
EXIT=Exit BFiler
BFiler> exit <rtn>
There is now a file called mel.bdt that contains the melittin alpha carbon data in a MacroModel useable form.
6) Creating data to be used in surface and volume studies.
Use the data entry capabilities of MacroModel to enter in the following three molecules. Be sure to save them by writing a file for each structure; these files will used again later in the exercise. Save the data in files called mol1, mol2 and mol3.
CH3 CH3
| |
CH3-CH2-CH2-CH2-OH CH3-CH2-CH-OH CH3-C-OH
|
CH3
molecule 1 molecule 2 molecule 3
Activate MacroModel by typing mmv30. Once in the actual 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 entered are all simple organic ones, use the main input window of the program for their creation. Use whatever method of data entry you feel most comfortable with, DRAW or GROW. Once the structure is complete and the hydrogens have been added, minimize the data with the MM2 force field (ENERGY, MM2, Start). Save the resulting structure to a file with the WRITE button and then return to the INPUT area. Clean off the screen and repeat this process until all three molecules have been entered and saved.
7) Determining the surface areas and volumes.
The determination of surface areas and volumes is done in the ANALYZ portion of the program. Select ANALYZ. Read in the first structure (READ, give your filename for the first molecule, mol1, press the RETURN key for structure number and enter y to have the work area cleaned off). Determine the surface area for the first structure by doing: SURFAC, VDW, Rad, respond with .85 for the radius value, use high density level 3 by pressing the Dens button until that level is reached, then select Start. Determine the volume of the same structure by doing: VOLUME, and Vol. Record the surface and volume values on the next page. Determine the surface area and volume for the other molecules by: reading in the new file, SURFAC, VDW, Start, then VOLUME and Vol.
molecule 1 surface area: ___________ volume: ______________ molecule 2 surface area: ___________ volume: ______________ molecule 3 surface area: ___________ volume: ______________
8) Looking at exposed charged groups
To explore this aspect of physical characteristics, a protein is needed. Since even small proteins are complex, turn off the atom labeling by selecting the A LAB button of the ANALYZ mode prior to reading in a protein structure to work with. Read in the protein crambin by selecting READ and entering crambin1 for the file name. Press the RETURN key for the structure number and give y to clear the working area.
To look at the location of the potentially charged amino acids in this protein, select DISPLA and then RChrg. Yellow denotes neutral amino acids, red is for acidic ones, and dark blue for basic amino acids. Use the Rot Y button to rotate the structure and determine if these charged amino acids are really on the surface of the protein or not. This button requires that an angle value be entered: use 45 degrees.
Note: At least on actual tektronix terminals, the Rot buttons get stuck in this angle and won't allow you to change the angle value. It can be difficult to remember what the orientation of the original structure was in and to identify it again when it reappears on the screen.
9) Showing the hydrogen bonding in a protein
To show the hydrogen bonding of in a protein structure, the protein needs to have hydrogens. Structures determined and stored in PDB normally don't have their hydrogen coordinates given unless they are very recent entries. Therefore, you must add these missing atoms before doing this determination. To help avoid problems, read in the crambin structure again. Move to the INPUT mode and select the H ADD button three times to add hydrogens to the entire structure. Notice how many atoms were added ( all those little green lines and H's off the original atoms).
Move back to the ANALYZ mode and select the HBOND button. The program will determine the number of possible hydrogen bonds, report their number at the top of the screen and draw them in as a dashed purple line on the screen. Notice how the hydrogen bonding occurs in just a few general areas of the molecule. Record below the number of hydrogen bonds found.
number of crambin hydrogen bonds: ______________________________________
Read in the crambin protein again. Strip the structure down to its backbone by: ANALYZ, SETS, MainS, DISPLA and Dis. Even with this small protein, the secondary structure is not all that easy to spot even with this backbone version of the structure. This is why color coding the data is so helpful.
To start the process, color the entire backbone white in the following manner: Mono, enter w for white, and then enter w again, this time to indicate use of only the working set of data. The displayed structure will be erased and redrawn in white on the screen.
Refer back to page 5 for the secondary structure information on crambin. Now, color the helical sections of the protein red. To do this, it is first necessary to locate the needed residues. Select GEOMTR for geometry mode, and then FRES. The FRES button will ask for a residue number and then for a chain label. Locate the staring point of the helix in this manner. Crambin has only one chain, so press RETURN to the chain query. The location of this residue is shown on the screen with a black label and a purple box drawn around a point on the residue. The FRES button is on until it receives two RETURNs in a row. Therefore, find the end of the first helix in the same way as you found the start. Once the second point is found, respond to queries from FRES by pressing RETURN until it stops prompting for input.
With these two points located, select SETS, and ResSq. ResSq will ask you to locate the starting point of the chain. Move the cursor over to the boxed residue that begins the helix and press the mouse button. A beep will come from the terminal if a real location has been found. With the start located, ResSq will ask you to locate the end of the chain, move to the boxed residue at the end of the helix and press the mouse button. ResSq will start to repeat the questioning process, ignore it. Move the cursor to Set1. You will be asked what you want to do. In this case enter d for depositing a data set. Select DISPLA and Set1 again. This time respond with r for retrieving a set. To color your data that has now been loaded into the working set of the program, select Mono, and respond with r for red and w for working set. The section you designated will be erased from the screen and redrawn in red.
Check to make sure that you have the right section coded for a helix by getting back into the GEOMTR mode and using NRES to number the residues that are still white on either side of the red portion of the structure. Correct any errors by going back through the coloring process.
Using the above information as a guide, color the other of the helical section of crambin red, its sheet sections yellow (y) and its turn aqua (a). Save the results of your efforts to a file called cram .
11) Working with your selected molecule.
Using your selected molecule, color code its secondary structure with the information you gathered at the beginning of this exercise. Use the previous section as a guide in your efforts. When you are finished, save the file called 7sel .
12) Doing superpositioning on simple molecules.
Since the molecules to be used here are all very small, read all three molecules used earlier to determine volume studies onto the same screen. Use READ, give the filename of molecule 1, mol1, press RETURN for the structure number, READ, give the filename of molecule 2, mol2, n to keep the existing structure on the screen, READ, the filename of molecule 3, mol3, and n to keep the other two structures on the screen.
To keep the various structures separate in the superpositioning process, color each of the molecules a different color. Get to the coloring portion of MacroModel by selecting ANALYZ, DISPLA. Now select Mol and move the cursor to one of the atoms in the first molecule. Pressing the mouse button should cause the terminal to beep at you, indicating the selection of a real location in the molecule. Select Mono, respond with a one letter code for a color (r - red, b - dark blue, a - aqua, y - yellow, g - green, o - orange, p - purple, w - white) and then with w to tell the program to only use the selected molecule for this process. Molecule 1 should be erased and redrawn in the selected color. Repeat this process with the other two molecules until all three are different colors.
With the molecules colored, select GEOMTR to get to the superpositioning portion of the program. To align the structures, use the hydroxyl oxygen, the carbon connected to that oxygen and the carbon to the left of that one.
A note about how superpositioning works in MacroModel. After picking the SuprA button, you are prompted to select atom pairs as tack points between the two molecules. The structure of the second molecule will be overlaid upon the first one. Therefore, if you wish the molecule on the left hand side of the screen to be the reference point for the alignment, select an atom in it first. The selection order must be maintained in doing this process. Always pick an atom in the first structure and then the second to get a tack point pair. A minimum of three tack points are required for each alignment.
Select SuprA and the program will prompt you to select atom pairs. Then move the cursor to first the oxygen on molecule 1 and press the mouse button. A beep will sound if the computer recognizes this as a real location. Move the cursor to the oxygen on molecule 2 and press the mouse button again. A beep followed by the drawing of a dashed orange line between the two selected atoms denotes a successful creation of a tack point. It takes a minimum of three tack points to do a superpositioning, so repeat this process using the carbons connected to the oxygen, and then the carbons one more step removed from oxygens to establish the other tack points. When the three dashed lines are shown, select RigSp. A value will be displayed on the screen showing how closely the tack points agree. The smaller this number is the better the alignment between the chosen tack points. You will be asked if you want to plot the results, respond with y. The second molecule will then be redrawn over the first one. Areas of agreement will appear to have the color of the second molecule, since on your terminal the first one has been overlaid with that color.
Repeat this process, using the combined structures as the first molecule, and molecule 3 as the second. Since you are using a combined structure, the software may get confused as to which structure you are selecting from. If you get the error message, PAIRS MUST BE ORDERED MOL1, MOL2 PICK AN ATOM IN MOL1, move the cursor slightly off the desired point and try pressing the mouse button again. It may take a number of times for the software to give you just a beep and no error message. Keep adjusting the cursor location until the point is accepted. After the three tack points have been created, select RigSp again and plot the results of your alignment. Write a file of your results called merge. Exit the program.
13) Doing superpositioning on complex molecules.
Copy over a log file for displaying a superpositioning demo. The logical name of this log file is position.
$ copy position *.*
To visualize a more complex superpositioning and do one yourself, get back into the MacroModel program with mmv30. Once in the actual program enter the name, position.log as the name of the log or script file. The log file will display the superpositioning of morphine and methadone. Morphine is shown in red and methadone in white. After the superpositioning process, the combined structures are rotated so you can view them from various angles. Methadone is a synthetic drug used in heroin treatment programs and morphine is an addictive pain killer.
At this point the log file stops and allows you to do this task for yourself. The file that you will need to read in is called together. Read in this file. On the screen will be three molecules, one in red, one in aqua and one in yellow. The molecules in yellow and aqua are very similar to another. Prove this to yourself by doing a superpositioning with these two molecules Use three similar atoms from the respective ring structures to do this.
Once this is done, read in the file again. This time use this data and superposition either the aqua or the yellow molecule onto the red one. The points of similarity are on the left-hand side of the molecule. With this first superpositioning done, overlay the other small molecule upon the first one using the hydrogens as the contact points. When this is done, WRITE the data to a file called 7coff
The file you have created contains an alignment of morphine, the red molecule, caffeine - the aqua molecule, and chocolate - the yellow one. Reflect on the possible meaning of this alignment.
14) Creating an alpha carbon trace (part 2)
Read in the file you created containing the alpha carbon atoms from the melittin. Clean off the screen by responding with y to the prompt about deleting the existing structure. Displayed on the screen will then be a collection of C's. From this data that you will be producing the alpha carbon trace. There are actually two chains displayed here, each composed of 26 alpha carbon atoms.
Because working with all the data displayed on the screen at one time would be confusing and could cause errors, use only a small portion of the screen at a time. This is done by selecting the Clip button at the upper right-hand side of the screen. Clip allows you select a portion of the screen to work with and then expands that selected portion to fill the entire working area. Once Clip is on (shown in green), move the cursor to a point on the screen that will serve as the lower left-hand corner of the area you desire to work with. Once in position, pressing the mouse button will cause a red indicator to mark the spot. Now move the cursor to the desired upper right-hand corner and press the mouse button again. After the indicator is shown, the entire working area clears and the desired section of the molecule will fill the screen.
To be able to connect the dots, the atoms shown need to be numbered. This is done by selecting the NUM button at the lower right hand edge of the screen. The atoms will then be numbered on the screen. To actually connect the dots (atoms), move to the INPUT portion of the program and use DRAW. Move the cursor to the lowest numbered atom on the screen and press the mouse button. The terminal should beep. Now move off to the second lowest number on the screen and press the mouse button again. If all has gone well, the two C's will disappear and be replaced by a line. Keep moving to the next lowest numbered atom until all the atoms that were shown on the screen are connected. With everything connected, move the cursor to Clip and press the mouse button twice. This will redraw the entire structure on the screen, showing what has been connected and what is still left to do.
Select a new area to work with via Clip. Then number the atoms again using ANALYZ, NUM and return to the INPUT section of the program to use DRAW to connect the atoms. Keep going through this process until all the atoms in the two chains have been properly connected. Remember these are two different chains, there should not be a bond between atoms number 26 and 27.
With both chains connected, color the chains with different colors so that you can tell them apart. Do this by using ANALYZ, DISPLA, Mol, selecting an atom on the desired chain to be re-colored, Mono, give the one-letter code for desired color, and respond with w for using the atoms in the working set. Choose some color other than green for this colored chain.
15) Superpositioning alpha carbon traces.
The melittin structure that you have been working with is supposed to be composed of two identical chains in different orientations. Go through the superpositioning process to confirm this. The first atom of chain one (atom 1) corresponds with the first atom of chain two (atom 27). Select at least three points on the two chains to make the alignment.
The superpositioning process is: be in the ANALYZ mode, select GEOMTR, SuprA, create three or more tack points, select RigSp, and respond with y to plot your results. Write out a file called mels.
16) Creating a data set to show superpositioning results.
Read in the 7coff data file. Clear off the screen to have a clean slate to work with. Select INPUT, ORIENT, Mol and then use the cursor to selection an exposed atom of the red structure. Now select Trans , enter x to move the red structure along the x-axis and enter in 20 for the distance. To get out of this process, enter * to the distance prompt and press the RETURN key in response to the direction query. The red structure has moved off of the screen. Select the Scale button and use the cursor to move to the lower left hand corner and press the mouse button. A red plus appears on the screen. Now move to the upper right-hand corner and press the mouse button again. The screen is redrawn putting all the data within the window again. After the red structure is again visible, repeat the process with the aqua one. Again move the structure along the x-axis and enter in a distance of about 10. Fine tune this location until the aqua structure appears to be in right in between the other two. When you are satisfied with the position of the aqua molecule, get out of the positioning process by entering * to the distance prompt and press the RETURN key in response to the direction query.
What is going to be done with this data is to compare the shapes of the newly structurally aligned molecules. There are some hydrogens on these structures that are going to cause problems when you attempt to use them in molscript. Molscript draws bonds solely on the basis of the distance between known atoms. The atoms with multiple hydrogen atoms on them [such as methyl groups or carbons with two hydrogens on them] are too close to one another and strange triangles result on the final images. To correct this change these offending hydrogens into fluorines. Go to ORGANI, select F from the atom selection portion of the screen with the cursor and then move over to each of the problem hydrogens and change them into fluorines by pressing the mouse button. Write your results to a file called pos. Exit the MacroModel program.
Convert your MacroModel formatted file to a PDB formatted one by running the output file through the mmodpdb program. Use the example given below as your guide. Create PDB formatted files of the cram.dat and 7sel.dat files as well.
$ mmodpdb THIS PROGRAM READS V1.5-2.0 MACROMODEL STRUCTURE FILES AND PRODUCES FORMATTED PDB STYLE OUTPUT FILES Enter MacroModel input filename: pos.dat <rtn> Enter .PDB output filename: pos.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 PDB format, it is time to modify the results of your conversion process. To produce the desire image you will need to do some customization of the PDB file. What is required is that you go through and pull out the fluorine lines and put them at the end of each respective molecule section. The three molecules are grouped in very distinctive coordinate regions. Change the UNK portion of these lines to be a distinctive term for each set of fluorines. Change the zeros between the X and the actual coordinates to a number consistent for each section: 1 for the first molecule, 2 for its associated fluorines and so forth. You can remove the CONECT lines if you wish, Molscript doesn't use them. Remove the lines with LP in them as well. These represent lone pairs of electrons (the double dots on some atoms) and while it is nice to know where there are, they only clutter up a Molscript image.
Edit the cram.pdb file to change all the C02 lines to have CAspace. Likewise make the same changes in the 7sel.pdb file.
Now ftp these three files (pos.pdb, cram.pdb and 7sel.pdb) and the mel.ca file over to your ribozyme account. Replace the bcsxx of the example with our own account name. User input shown in bold type.
$ 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 week7<rtn> <CWD command successful. RIBOZYME.VADMS.WSU.EDU> type ascii<rtn> Type: ASCII (Non-Print), Structure: File, Mode: Stream RIBOZYME.VADMS.WSU.EDU>put pos.pdb<rtn> To remote file:<rtn> <Opening ASCII mode data connection for 'pos.pdb'. <Transfer complete. RIBOZYME.VADMS.WSU.EDU>put cram.pdb<rtn> To remote file:<rtn> <Opening ASCII mode data connection for 'cram.pdb'. <Transfer complete. RIBOZYME.VADMS.WSU.EDU>put 7sel.pdb<rtn> To remote file:<rtn> <Opening ASCII mode data connection for '7sel.pdb'. <Transfer complete. RIBOZYME.VADMS.WSU.EDU>put mel.ca<rtn> To remote file:<rtn> <Opening ASCII mode data connection for 'mel.ca'. <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. Once there, move over to the week7 subdirectory location.
17) Creating the various images.
image #1:- superpositioning data
In the files that were copied over at the beginning of the exercise is a template control file for creating a Molscript image of the superpositioned data. This file is called pos.in and it is up to you to modify it with pico to reflect the actual terms you used for the fluorine line groupings. In this file you will notice that the size of the fluorine atoms and their color has been changed to mimic that of hydrogen atoms. The only difference will be that the bond lengths will be a little longer than they should be.
% pico pos.in % molscript <pos.in> (your lastname)-pos.ps % lpr (your lastname)-pos.ps
Not all software shrinks structures when it connects alpha carbons. This is the main method of creating secondary structure images in Molscript. Process the original data file containing just the melittin alpha carbons on the following manner.
% molscript <mel.in> (your lastname)-mel.ps % lpr (your lastname)-mel.ps
A template Molscript input control file called cram.in has been created to give you practice in going through and changing the parameters that control the drawing of a secondary structure image. In this file you will need to change the set planecolour lines to the desired colors and add the necessary lines to control the drawing of the actual secondary structural elements. Remember to have coil sections connecting the helical, sheet and turn regions. These coils sections should xxxx. Color the helixes purple, any sheets cyan and the turns yellow. Use pico to make these changes. Refer to the secondary structure data on crambin you collected on page 5.
% pico cram.in % molscript <cram.in> (your lastname)-cram.ps % lpr (your lastname)-cram.ps
A generic template file has also been created to handle the creation of an image for your selected molecule file. In this file you will need to again change the set planecolour lines to the desired colors and add the necessary lines to control the drawing of the actual secondary structural elements. Remember to have coil sections connecting the helical, sheet and turn regions. Color the helixes red, any sheets green and the turns . Be sure to have the correct chain identifiers if you need them. Use pico to make these changes. Refer to the secondary structure data on your selected molecule you collected on page 5.
% pico select.in % molscript <select.in> (your lastname)-select.ps % lpr (your lastname)-select.ps
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 four image files you created to teacher as well.
% mv week7m.week7m (your lastname).week7m % pico (your lastname).week7m % rcp (your lastname).week7m teacher@ribozyme:receive % rcp (your lastname)-pos.ps teacher@ribozyme:receive % rcp (your lastname)-mel.ps teacher@ribozyme:receive % rcp (your lastname)-cram.ps teacher@ribozyme:receive % rcp (your lastname)-select.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.