The program was developed and tested most recently on an SGI Indigo2 with XZ graphics. It should function on a variety of graphics configurations, including 8 bitplane systems (Z-buffer highly recommended). IRIX 4.0.1 or newer is required.
If you do not have the Developer Option with your SGI machine, binary code may be available through ftp. The best performance will be obtained by compiling on your own machine, however.
Press and hold the right mouse button at any time during the main program to bring up the menu. The options are described below. Menu options that are currently selected will have a check mark next to the menu item (for example, a check will appear next to 'Display 2nd molecule' when the 2nd molecule is being displayed). Selecting this option AGAIN will remove the check mark and also reverse the status of the function. When a menu option is unavailable (for example, 'overlap molecules' when no molecules are loaded) it will be gray, and you will be unable to select it until it becomes appropriate.
You may also type directly on the Path: and Name: lines. A white underscore bar is shown at the end of the currently active line. Backspace to delete characters, or use the 'CLEAR' button to clear the text (name only). Press 'OK' when finished, 'Cancel' to quit without making a selection. The 'CLEAR PATH' and "CLEAR FILE' buttons function as the names imply.
Pressing the 'LIST DIRS" button will open a window showing you a list of other directories that you have visited. Press the left button on one of them to replace the current path with the selected on. The directory list is saved in the session file.
The program will warn you if you ask it to write over an existing file, asking for confirmation.
If you are unsure of the current format, check the menu. A check mark is placed next to the current format for each type. In addition, each file requester will inform you of the format it expects to load.
Coordinates and topology for each of the two molecules can be in different formats.
Be careful when writing coordinate files- the write function always uses the CURRENT format, which may be different from that of the original coordinate file (if you have changed it since loading the original file).
Note that since PDB and CRD formats include atom names, the distance algorithm can be used for calculating bonds. AMBER files do not contain this information, so the program will not be able to assign atom types and colors, and the calculated bonds may be incorrect. Load an AMBER topology file (under Load Connectivity described below) to make sure the program displays the correct information.
The toolbox is activated any time the LEFT mouse button is pressed. If the pointer is over the toolbox at the time of pressing the LEFT button, the structure will be transformed according to the current selection. The rotations and translations are sensitive to the distance of the pointer from the center- the farther away from the center you press, the faster the structure will move.
Size will zoom in and out, lines changes the number of pixels used to draw the bond lines, and reset view returns to the original settings for size, rotation, and translation. It does not affect linewidth. Note that rotations are done in the screen-fixed coordinate system, and the axes in the upper corner reflect the original axes in the first molecule.
The toolbox can be moved to wherever is most convenient by simply grabbing the window at the top title bar (using the left button) and then moving and dropping it.
The letters 'R', 'T' and 'S' above the 'Mouse Mode' label allow you to quickly change the mouse mode, as described below. A red box appears behind the currently selected mode.
Keep in mind that the toolbox is active even during a dynamics movie.
Do not confuse this 'pick' with the selection of particles using the mouse, which displays information on the screen! That type of picking (hereafter called selecting) is described below.
The above line stands for (in brackets we wrote the corresponding expression)
pick particles 1 to 60 (#prt 1 60), or (|) like a good chemist (chem)
pick all particles of the monomer (mono) alanine (ALA) anywhere this
mono name is found, but you should pick this under the .and.
selection (&) of chemical (chem) particles (prtc) that are
called (CA), then you should remove (!=) from the selection
monomer numbers (#mono) from 2 (2) to 3 (3). and this is all (done).
The pick line is of the format
pick A lexp B lexp C lexp ... done
don't forget the 'pick' and 'done'!
where A-C are selection commands and lexp are logical expressions
note that the line must begin with 'pick' and end with 'done'
#prt - defines range of particles to be picked, e.g. #prt 1 6 #mon - defines range of monomers to be picked, e.g. #mon 1 3 chem - An indicator for "chemical" notation will be used. prtc - select by chemical name of particle mono - select by chemical name of monomer examples: "chem prtc CH3E" "chem mono HEME"Modifications added in MOIL-View include:
#sid - picks side chain atoms by mono # -
anything BUT: C, O, N, H, CA, NH, HN, HA
#bac - picks backbone atoms by mono # - C, O, N, H, CA, NH, HN, HA
#ba2 - picks backbone atoms by mono # - C, CA, N, NH
old commands with easier to remember names: #atm - identical to #prt #res - identical to #mon atom - select by chemical name of atom (same as 'prtc')
You may also use '*' as a name completion wildcard, eg. CH* would pick CH2, CH, and CH3. You are not allowed to have any characters after the wildcard. Note that *H will NOT select 1H and 2H (but will instead act like * and select everything), and C*N will act like C*.
Pressing the MIDDLE mouse button while near a particle will place a circle around it. The screen will display the monomer and particle information. Once a particle is selected, the structure can be centered with this particle at the origin (see options submenu above). This centering will remain in effect EVEN DURING A MOVIE. This can be helpful for tracking a particular particle during a dynamics run.
Selecting a second particle will give the distance to the previous selection, and a dotted line will be drawn between the two. Both the line and the displayed distance will be updated each dynamics frame. This can be useful for monitoring distances during dynamics. Note that if the two particles are in different molecules, a line will NOT be drawn, since the molecules are kept in different coordinate systems. Selecting a third and fourth particle will display the current angle and torsion, along with the particle names for the particles that were selected.
At the bottom of this document is a complete list of the menu options , with hypertext links to the appropriate section of the manual.
There is also a second load coordinate command, used to load a second structure for comparison. The second molecule does not have to be related to the first. Note that many program functions (dynamics, spheres, hydrogen bonds) function only on the first molecule. The second molecule is mostly useful for overlap and comparison (see below).
When a second molecule is loaded, many menu choices can be applied to either molecule. A window will open and ask you which molecule to change, (1 or 2), and some options will ask (1, 2 or both).
4 (4 particles) 3 (3 bonds) 1 2 (bond 1 to 2) 2 3 (bond 2 to 3) 3 4 (bond 3 to 4)You can also choose to write the current coordinates to a file from this menu. This will apply any rotations or centering that have been made, but not scaling or translation. The coordinates are also changed after overlap and dynamics. Read the warning below concerning writing coordinates after changing the default file format type.
You may also load and save 'session' files (described above) in this menu.
Set file formats alows the user to set the default formats for reading and writing files. The supported formats are described above. The first time a file of a particular type (coordinate, trajectory, etc.) is loaded, the program will ask the user to choose the format. From that point on, that will be the format expected unless the user changes it using this menu option. The file browser will always state the current format that the program expects.
The format of each file is saved in the session file so that the files can be properly read and restored.
Show Toolbox controls the display of the toolbox (for rotations, etc). The default is ON. See 'about the toolbox' below for more information.
Status Info turns on and off the display of information about the selected particles, such as molecule #, monomer and particle name. It also shows the distance to the last particle that was selected, and the name of the last particle. Selecting three particles will show the angle value, and four selections will return a torsion angle value. The center mouse button is used to actually select the particle. All information is displayed in the lower left corner, and a circle is drawn around the current selection, with a dotted line drawn to the previous selection. Particles from either molecule can be selected.
These particles are NOT necessarily those used to plot trajectory data! This is different from the behavior of previous versions of MOIL-View. The particles selected at the time the plot is made are used, and even if the selection is changed, the particles used for the plot do not change. This allows the user to select different particles for distances and angles, for example. To change the particle definition for a plot, simply re-open the plot as described below in the plot sub-menu. The current atom numbers used for a particular plot are always displayed in the plot window's title bar.
The 2nd molecule submenu contains options for controlling the second structure. Display turns on and off the display of the second structure described above. Delete will actually remove the second molecule from memory. Flash will toggle the flash mode where the program alternates between the display of the first and second molecule every few seconds. This can be useful for comparison of two structures.The rate of flashing can be set under the set parameters menu described below.
Bond Algorithm creates your structure based on 1) a distance algorithm in which any two atoms closer than the sum of their covalent radii are bonded, or 2) based on connectivity information from the connectivity (or topology) file. When a coordinate file is loaded the program will ask if you want to use the distance algorithm. If the current connectivity file does not match (in number of particles) a newly loaded coordinate file, the program will also ask if you want to switch to a distance algorithm. If not, you will need to load a new connectivity file. Option 3), consecutive atoms, creates bonds between each set of consecutive atoms. This can be useful in some circumstances, such as displaying a coordinate file that contains only the alpha carbon atoms of a protein.
The bond algorithm can be chosen separately for each of the two molecules, and the information will be saved in the session file.
The bond list is assumed constant during dynamics movies, and is NOT recalculated for each frame. You may need to modify the code if you are changing bonds during the dynamics.
Center Object allows you to center the structure at an origin calculated at either the center of mass (CM) of the structure, or at a selected atom. You must select the particle (see below) and THEN choose center on selection for this to work properly. The centering will remain effective even during a dynamics movie. The centering can be removed using don't center. This option will work with either molecule.
The Solvate menu allows you to add solvation to your molecule. This option requires that you already have a file (in CRD, or PDB format) containing the coordinates of the water molecules. This coordinate set will be used to add either a solvation shell (of user defined thickness) or a box (suitable for periodic boundary conditions). A box outline can be drawn to aid in determining the proper box dimension for your system. After the parameters are provided, the coordinate sets are overlapped and any water molecules that overlap the original molecule are removed. The program also removes any water molecules outside the shell or box boundaries. At this point you should save the coordinates to a new file.
Note that the 'Draw box outline' will also display a box that will be updated during dynamics, if the trajectory file contains this information (AMBER PBC). It will also draw the correct box size if the information was contained in the AMBER restart file.
Movies has two options. They are described below.
Generate: Here you can make a movie, just like in Dynamics described below, except that each frame will be compressed and saved to your choice of disk file. This file can get VERY large.... This is mostly useful if you have a very complicated scene and not very expensive graphics hardware! The delay time to render each frame will be replaced with the time to decompress and display the file, which is usually much shorter.
In the current version, only the lower left portion (640 by 480 pixels) of the physical screen is saved. This is done to maintain compatibility with early SGI video output devices. Current harware such as Galileo Video can convert the entire screen to NTSC format, but the program does not yet support compression for these devices due to memory constraints. Send me e-mail if you want to try full screen movies on your system.
Watch: This will retrieve and uncompress frames from a disk file made with the generate. The playback speed using this method is essentially independent of the complexity of the structure, unlike the actual sphere rendering. This is mostly useful to make videos of large numbers of highly detailed spheres, to be played back at reasonable speeds. If you are lucky enough to have very fast SGI graphics, this may not be necessary. Due to the large size of the movie file, it is most efficient to use a local disk for playback files.
Hydrogen Bonds contains selections that allow you to find and display hydrogen bonds using dashed lines. Again you will be allowed to 'pick' which section of the molecule should be searched for h-bonds. You are also allowed to select the color to use for the dotted lines. The criterion for valid hbonds can be adjusted: distance through the option described below , but currently the angle must be changed through the code in findhb.f. Turn Off will remove the hydrogen bonds.
Video Timing:
This option is for users of NTSC monitors
(genlock or videotape). Choosing this option toggles between
hires and NTSC timing. In NTSC mode, only the lower left
quadrant of the screen is shown on your NTSC monitor.
This mode is useful for recording a dynamics movie to
videotape to impress your friends, colleagues, and
funding sources. If you do not have a genlock, this can be
very annoying if chosen accidentally. Comment the line in
source/main.f that controls this command (a call to the
toggle() subroutine).
I COLOR OPTIONS:
This is where you can choose what colors are
used for the particles, and which particles are displayed.
User Defined: using a MOIL-style 'pick' command (described above), you can assign new colors to any particles. Press the return key to move to the next line. The first three lines in the requester are for the red, green and blue values. You can mix these like paint to form millions of colors (depending on the number of bitplanes in your system). Choose a red, green and blue and then give a pick command on the fourth line. Any particles 'picked' will be given the color you chose. Choose black (0,0,0) to turn OFF display of a particle with a black background, and white (255,255,255) on a white background. Lines and spheres for background-color particles are not drawn. This can speed up sphere rendering dramatically. It is sometimes useful to turn everything OFF first (0,0,0) and then turn ON the particles you want to show.
In addition to typing in a specific red, green or blue value, you can adjust the sliding box over the color bars to choose the proper value. A preview of the current color mix is shown underneath the color bars.
Select 'HELP ON' from the color selection window if you need a reminder on the 'pick' syntax. Select 'LIST PICKS' to open a window listing previous pick commands that you have used (along with some common selections). Click on one of these with the left mouse button to transfer it to the current pick: line.
Restore Default returns you to the default colors. Change the file 'setparam.f' if you want to change the default values. A window will open and ask you to enter a 'pick' command to select which atoms should be restored.
Backbone Only: this will show only the alpha-carbon, carbonyl carbon, and nitrogen of the protein backbone. Currently, it turns off everything else, and leaves the backbone with its current colors. This may give unexpected results if the backbone is not already displayed.
Currently, the atom names that define the backbone are hard-coded in the program as C, CA, N, H, and O. Modify the code in main.f to change this default behavior.
No hydrogens : this will remove all atoms whose names begin with H.
No water: this will remove all water- monomers with names WAT, TIP or HOH.
Close Waters Only: This turns off all waters not within the hbond cutoff distance from non-water molecules. The cutoff criterion can be adjusted in the change parameters menu. Waters are monomers that have WAT, HOH or TIP as the first three characters. Updating which waters are 'close' can be done optionally during dynamics (but may be slow). If the close water option is selected, a requester will open before a trajectory is displayed asking if the user wants to update the selection.
Close Residues Only: This turns off all residues not within a user-specified distance from a selected group of atoms. The program allows you to input a cutoff distance and a 'pick' command selecting the initial group of atoms.
Transparency allows you to set the alpha values (0-255) which control particle opaqueness (on machines that support this alpha blending). Higher values are more opaque. The transparency feature does not work perfectly. If you don't have alpha support on your system, dot spheres give a similar effect (see below).
Pick HB color performs the same function as described above, and is also placed here simply for convenience.
Background Color: This allows you to choose white or black as the background color. If the background is black, any black (color 0,0,0) particles will NOT be displayed, and if white, color (255,255,255) will not be displayed. Use these color choices to keep certain portions of the molecule from being displayed, or printed in the postscript option. Switching between background colors automatically changes the color of particles that are not displayed. While the postscript DRAWING option will always be on a plain page background (white), the postscript BITMAP image WILL save the background color.
All color information (for both molecules) is saved in the session files.
OVERLAP MOLECULES:
Best fit RMSD
allows you to issue 'pick' commands to
select particles to be used to overlap the two molecules.
The structures will be overlapped (using the
Kabsch[3]
algorithm) to minimize the root mean square deviation
(RMSD) of the picked particles.
You must choose at least 3 atoms. Any errors, such as
zero determinant of the transformation matrix, will be
written to standard output. After overlap, both
structures will be active in the toolbox (see below).
If desired, a different set of particles is chosen for the
calculation of the root-mean-square deviation of the
two molecules. For many purposes, simply click on 'no' when
asked if a different pick is desired for the RMSD calculation.
In some cases, such as fitting two proteins on the full backbone
followed by calculating the RMSD of a loop, it may be appropriate
to fit on one set of atoms but calculate the deviation for another
set. Note that this does NOT minimize the RMSD between the atoms.
You can use the same 'pick' command for both molecules, which will apply the same pick to each molecule. Note that this does NOT mean that you will pick the same particle numbers, or even the same number of particles. For example, if you pick all alpha carbons and the two molecules have different sequences, you will pick different atoms. You must pick the same number of atoms in each molecule in order to perform the overlap. If both molecules correspond to the same system, using the same pick command will pick the same atoms.
You may also choose DIFFERENT pick commands for each molecule. An example of this might be to overlap the final segment of two proteins that differ in initial segments (eg. overlap monomers 24-25 of one structure with monomers 28-29 of the other structure).
Select the 'HELP ON' box from the overlap window if you need a reminder of the pick syntax. Select 'LAST PICKS' for a list of previous picks, and use the left mouse button to select one of them as the current pick command.
After defining the atoms to overlap, the program will ask if you want to restore the original origin. This is done because both molecules are centered at the CM of the selected particles prior to fitting. In some cases you may want to 'uncenter' the molecules after the fit has been performed.
If you perform an overlap prior to watching a dynamics trajectory, you will be given the option to re-fit molecule 1 to molecule 2 automatically for each new frame using the same parameters that were previously defined.
This same basic procedure also applies to defining the overlap for the trajectory overlap plot, 2D-RMSD plot and cluster analysis.
RMSD only functions very similarly to the
best fit RMSD function described above, but in
this case the RMSD
is calculated directly from the current coordinates with no fitting
or attempt to minimize the RMSD.
Plots
The Plots menu provides options for generating postscript
files suitable for printing images of your molecule. In addition to
these images, several other types of data can be printed, such as
data plots from trajectory information and 2D-RMSD plots.
In MOIL-View, there are two ways to get a paper copy of your image. First, you may choose the Postscript Drawing command. In this case, specific postscript drawing commands are used, and the resolution of the image will depend only on your printer. However, this option currently does not provide all of the imaging options available in MOIL-View, so another option, Postscript Bitmap is provided. In this case the postscript image is created directly from the screen image. While this provides a better reproduction of the actual screen image, the resolution of the computer monitor is usually much lower than that of typical printers, resulting in a less smooth image than provided by the Drawing option. There are two further options under Postscript Drawing, normal or ball and stick. Normal drawings are described below. Ball and stick drawings are similar except that each particle will be drawn as a circle 1/10 the size of its VDW radius. This circle is drawn in addition to the lines connecting bonded particles.
This option generates postscript output for a simple hardcopy of the display. The structure will be in the current view, using lines. Circles are used for any particles that were spheres. You will be asked whether you want to depth-cue the image. If you choose this option, the lines for particles farther from the screen will appear lighter, fading into the page. You can also choose to use the particle colors, or use black for all particles. Note that, even if particle colors are NOT used, particles that are the background color WILL NOT be printed. Color choice here means that particle colors will be taken into account, otherwise all particles are the same color. Whether you actually get color depends on your printer. Colors will show as gray scales on B&W printers, and full color if your printer supports it.
The thickness of the sticks is related to the screeen line width chosen in the toolbox. Ribbons, spheres and hydrogen bonds will be printed if they are displayed on the screen. Text labels will also be printed (see below).
After creating the postscript file, you must send it to your printer using 'lpr' or whatever command is appropriate on your system.
The Postscript Bitmap option will take the entire displayed image, and convert it to a postscript bitmap file. These files are VERY large- 2 megabytes for B&W and up to 6mb for color. In addition, they tend to take a very long time to print. The advantage to this method is the the image will be exactly like your screen image (within printer limitations), with proper sphere shading and interpenetration. It makes little difference for line objects. Again, you are responsible for sending the postscript file to your printer (and deleting it when you are finished!).
Note that the color/gray option here determines whether full color information is saved in the postscript file, or only gray scales. This is different from the postscript drawing option, where the 'color' choice determined whether particle colors were used at all, and a single file was appropriate for color or black-and-white printers. Here, particle colors are always used. Full color bitmap files are 6+ megabytes in size, and gray scale only 2+ megabytes, so choose the type that is appropriate for your printer.
TRAJECTORY 2D-RMS: Trajectory 2D-RMSD plots can be generated from two sources: a data file that the program can load containing all of the RMSD values, or values calculated from a dynamics trajectory.
Choosing to calculate new RMSD values will call the standard dynamics routine described below , but data will be collected for the RMSD of each frame in the trajectory to every other frame. If you do not have a currently defined overlap from overlap molecules, the program will prompt you for a pick command to select the particles to overlap, as described above for simple overlaps. You may select the same or different sets of atoms for the fitting and RMSD calculation.
It is important to note that the program must save the coordinates of each of the 'picked' atoms (not ALL atoms) for each frame of the trajectory. The limits on the number of atoms and number of frames for this option are defined in the source code in LENGTH.BLOCK, and recompiling is necessary to change the default sizes. The parameters are named MAXRMSPT and MAXRMSFR.
This option will also result in the loss of the second molecule, if one is currently loaded.
The program will use the standard file browser to obtain the trajectory file name, and then present the user with the standard dynamics options described previously. Skipping frames results in a smaller plot that covers the same time period, but with reduced resolution- a quick fix for trajectories that exceed MAXRMSFR.
After the trajectory has been read and displayed, the file browser will request a name for the new postscript file. Next, you must choose whether to print larger RMSD values as increasingly darker or lighter shades of gray. Another choice involves 'smooth' shading- where the RMSD values are directly mapped to gray values, or discrete shading- where four ranges of RMSD values are used. In the case of smooth shading, you must choose a cutoff value for the high end of the scale- all values above this will be considered the same, and those below it will be smoothly shaded. For discrete shading, you must choose three cutoff values, which result in the ranges: 0-LOW, LOW-MIDDLE, MIDDLE-HIGH, and HIGH+. In either case, a legend is printed on the page for reference, along with the appropriate file names and the 'pick' commands used to generate the RMSD values.
Once again, you are responsible for sending the file to your printer/previewer. The program will ask if you want another plot (changing shading or cutoff options), and allow you to create a new plot without needing to re-calculate the RMSD matrix. It can be useful to load a postscript previewer and examine the plot, refining the parameters and re-plotting before returning to the main program function.
Finally, you are asked if you want to save the RMSD data directly to a file. This data may be useful as input for other programs or can be used to re-generate a plot without recalculating the data. The data is saved one value to a line, starting with frame 1 and continuing to the last frame, printing the RMSD to each frame (including itself). This provides (number of frames)^2 data points (which can turn into a very large file).
The Plot Trajectory Data menu allows you to create or remove windows that plot data from a dynamics trajectory. Distances, angles and torsions (such as are already displayed in the lower left corner of the screen) can be plotted (for molecule # 1 only, however). After opening a plot, the program will ask whether points or lines should be used to draw the data. Points may more useful than lines for torsion values where, for example, a line between + 180 and -180 degrees may not be drawn in the direction of the true transition.
If desired, the overlap RMSD can also be plotted as a function of the trajectory time. In this case a second coordinate set (for overlap) should be loaded, and the overlap molecules menu choice should have been used to 'pick' the particles in each molecule for overlap. If a second coordinate or an overlap choice have not been defined, the program will allow the user to do so at this point. The user may also use the current first molecule as the reference if a second molecule is not loaded.
A Ramachandran-style plot can be made (phi and psi angles for a single protein residue). The user has the option of retaining all data points for the full trajectory (providing a plot of the cumulative conformational space sampled), or displaying only the current point, to show the instantaneous sampling. When the plot is opened, the program looks for consecutive bonds of the type C-N-CA-C (phi) and N-CA-C-N (psi) in which the CA atom is in the same monomer as the currently selected particle. If there are problems in the monomer numbering or particle names, the program may not be able to find these torsions, and attempting to create the plot will be unsuccessful.
It is important to note that the data in the window represents the particles that were chosen at the time the plot was created. These particles are displayed in the title bar of each plot window. In this manner, the on screen particle selection can be changed without affecting a current plot. If the user decides to plot a new set of data, the plot should be re-opened after selecting the new particles, and the trajectory should be viewed again to make the data represent the new particle selection.
In addition to data calculated from the trajectory, the user can load an external data file to plot. This can be useful to monitor the trajectory while comparing to data that can not be calculated by MOIL-View. The data file must have a single data value per line.
After drawing a plot of the data, data can be saved to disk using the save data menu option. These files can then be used for further analysis or plotting outside of MOIL-View. The data file will contain the frame number and data value for each point, with one point per line.
Simple postscript plots can also be created to print a hardcopy of the plot using the save postscript plot menu option. As with previous drawings, you need to send the postscript file to the printer by yourself.
Only one plot of each type can be active at a time- selecting 'create plot' when the plot is already active will simply close the plot and re-open it (possibly using a new particle selection). This does allow you to change the plot options, such as points vs. lines and the particles that are used to define the plotted value.
The Residue Contact Map menu option will generate a postscript file for a simple contact map based on particle distances. You issue a 'pick' command for the range of monomers to use for the map, and the program calculates distances between particle pairs in this pick. A postscript file is generated which shows the pattern of MONOMER contacts. Any monomer pair with at least one particle pair 'touching' will be considered to be in contact. The distance used for contact can be changed in the 'change parameters/contact map cutoff' submenu (see below). As with the postscript files described above, you need to send the file to your printer using the command appropriate on your system.
The HH Contact Map works similarly to
the Residue Contact Map described above, except that pairs of
hydrogen atoms are considered. This option is currently under
revision.
DYNAMICS:
The View Trajectory
option allows you to use a CHARMm or MOIL
DCD type, MOIL PATH, or AMBER trajectory file
compatible with the current structure to view dynamics
(for molecule 1 only). After selecting the file using
the file browser
, a window will request you to give the
delay between frames, start and end frame number,
number of frames to skip between each frame displayed.
DCD files contain information such as total number of
frames in the trajectory, but AMBER files do not. Only
formatted AMBER trajectory files are supported, while
DCD and PATH files are unformatted (binary).
You may also choose whether to 'cycle' the movie, which returns to the first frame after the last, continuing until the user interrupts.
AMBER users need to make sure that they choose the proper file format- AMBER or AMBER PBC. AMBER PBC should be used for simulations with periodic boundary conditions, as these files contain extra information on the box dimensions. Use of the wrong format will result in the structure turing into a MESS.
To pause the movie, press "P" (capital p) on the keyboard. During pause, the molecule orientation may be changed using the mouse or toolbox. Press 'Q' to quit the dynamics or 'C' to continue. In addition, pressing the RIGHT mouse button during dynamics will bring up a window asking if you want to either cancel or continue the movie.
When you discontinue the movie, the current structure is no longer the INITIAL coordinate file, but the LAST SHOWN from the dynamics file. Re-load the coordinate file if you want the original coordinates. During the movie, the current frame number is displayed in the bottom right corner.
Any centering choices will be repeated on each dynamics frame.
If a distance line is shown, it (and the calculated distance shown) will be updated for each frame. Angle and Torsion values will also be updated for each frame.
Ribbon positions will be updated during dynamics, but since hydrogen bonds can be slow to calculate, the user can decide whether to update these bonds during dynamics. If hbonds are active, a requester will open and allow the user to make this choice.
The user can also decide whether to update the list of close waters for each dynamics frame if color options/close waters was previously selected. This update can be slow for large systems.
If a second molecule exists and an overlap has been performed, the program will ask if the user wants to repeat the overlap procedure for each dynamics frame. This will be done automatically if the user is plotting overlap data for the trajectory (see plot trajectory data).
It is important to note that, during a movie, coordinates for all frames are not being saved, but the movie is shown WHILE the dynamics file is being read. This may change in the future. Some performance deterioration may be noticed for large structures, ESPECIALLY IF THE TRAJECTORY FILE IS ACCESSED OVER THE NETWORK.
CLUSTER TRAJECTORY:
The program provides a simple cluster
analysis function, based on a
2D-RMSD matrix generated
exactly as described in the preceding section.
A pick command
must be provided, and the trajectory file is
selected using the file browser. The standard dynamics options
entered next. After the dynamics are completed, the RMSD values are
calculated. You may then save the entire data set to a
file as described previously.
The clustering proceeds as follows: Each frame is initially placed in a cluster by itself. The program next prompts the user for a cutoff value to be used in the clustering. For each pair of clusters, the average RMSD between all pairs of structures in the two clusters is calculated from the RMSD matrix data. We then focus on the pair with the lowest average RMSD (the most similar pair). If the average RMSD of this pair is less than the specified cutoff value, the two clusters are combined. This process of calculating average RMSD and combining clusters is repeated until all cluster pairs have an average RMSD greater than the cutoff value. Then, a 'representative' structure is found for each cluster. This structure is the one that has the lowest average RMSD to all other members of the cluster to which it belongs.
The information about the number of clusters found and the number of structures in each cluster is written to the standard output in the present version. The user may then decide to try a different cutoff value to see how the clustering is affected. If a nother cutoff is not desired, selecting 'NO' will open another window presenting four options: PS1, PS2, TRAJ and NONE. Each will be described in detail below. While this window is displayed, waiting for the user choice, the molecule may be rotated, scaled, etc. just as it normally can be from inside the main program. This is important for re-orienting the molecule for postscript plots, as will be described below
The first option, 'PS1', will save a single cluster to a postscript plot, identical to that obtained using postscript drawing. The program will ask whether the user wants to plot ALL of the structures in the cluster, or only the single 'representative' structure. The program then asks which cluster number to print (from the clustering info written to the standard output), a name for the postscript file, and the standard postscript plot options. The program will then go back through the original trajectory file and extract the full coordinate set for each of the desired structures, and then write the plot to the file.
It is important to note that this postscript plot will use the current view of the molecule, and also the current color selections, just as the standard postscript drawing would use. It is not currently possible to change the color selection while inside the clustering routine, but the view can be changed while the option window is open.
The second option after clustering is labelled 'PS6'. This will create a postscript drawing similarly to that just described, with the exception that instead of a single cluster, the 6 most populated clusters will be drawn separately on a single page. Each cluster will be labelled with cluster number and number of members in the cluster. Again the current colors and view of the molecule are used.
The next option 'TRAJ', saves all of the structures in a single cluster to a new trajectory file. The program will request the cluster number and a new trajectory filename and format. This trajectory file can then be used as input to re-cluster or sub-cluster the original cluster(s).
After any of the options has been performed (except 'NONE') the program will again present the same options. In this manner the user can create multiple postscript plots from different views, plots of several clusters, and so on.
If the last option, 'NONE', is selected, the program will ask if the user wants to save some of the clustering information to a file. This information includes cutoff values, RMSD values between representative structures of cluster pairs, the cluster number to which each of the structures belongs, the RMSD of each structure to the representative structure of its cluster and the RMSD value between each pair of clusters that were combined. Examination of these RMSD values can be useful in determining an 'natural' cutoff value.
At this point the program will ask if the user wants to try a different cutoff value. If so, the program will re-cluster and present the same options for saving postscript files, trajectories and cluster information. Selecting 'NO' will return the user to the main program.
Be patient- due to the large number of calculations that are necessary, clustering can be quite slow. Try clustering a smaller number of frames.
MODIFY TRAJECTORY
This option allows you to change your trajectory
file in many ways. The options described below can also be
combined to modify several aspects of the file in a single pass.
The program will first ask if you want to save the modified trajectory to a new file. If you select 'no', the new trajectory will be displayed but not saved.
Next, the program will ask if you want to save the trajectory to a postscript file. This will create a printable file with all of the structures of the trajectory superimposed on a single page. Output is similar to that obtained for a single structure in the postscript drawing option described above. You may also specifiy that the program should skip a certain number of frames between each saving to the postscript file. This can be useful for paring down very large trajectories that contain too many frames to reasonably view on a single page. Skipping 4 will result in printing frames 1,6,11, etc.
Next the program will ask if you want the trajectory overlapped. This functions just like the single-frame overlap trajectory function described previously. If a second coordinate set is loaded, it will be used as the reference coordinates for the overlap. If one is not present, you may load a second molecule OR you may simply use the first coordinate set as the reference (which will copy it to the second set). The program will prompt you to make a choice. As usual, pick commands are required to specify the particles to overlap.
Next, a cutoff value can be specified such that only structures with an RMSD less than the cutoff will be saved (in the postscript file and in the new trajectory file).
The next option is to decide which atoms should have coordinates saved in the new trajectory file. One possible use is to save only non-water atoms to reduce the size of a solvated trajectory. Keep in mind that such a trajectory will no longer match the coordinate and topology files that are used for the original trajectory, and you may need to create a new coordinate and/or topology file for the program to be able to use this new trajectory. A standard pick command is used to choose which atoms to SAVE.
The file browser now opens to allow you to choose the OLD trajectory file. Select it as you would any file.
Another option is to calculate the average coordinate set over the full trajectory interval selected. If this option is chosen, the structure after the trajectory has been displayed will be the cartesian average. This usually only makes sense if the individual frames have been overlapped. You may want to save these coordinates in a new file.
The next option is whether to use a running average of frames for the new trajectory. The user may specify how many frames should be combined to produce the running average. For example, if the user chooses a value of 5, frame #1 in the new trajectory will be an average of frames 1 through 5, frame #2 will be 2 through 6, etc. This has the effect that high-frequency motions are removed, often making the large-scale motions easier to observe.
The standard dynamics option window opens next, allowing you to choose which part of the original trajectory should be used. Skipping frames will result in a smaller trajectory file that still covers the same time period as the original but with reduced resolution.
The output format of the new trajectory file can be chosen next. Note that writing an AMBER PBC format file when the original trajectory did not contain box size information will not place correct box sizes in the file. In some cases, however, you may need to have a file in this format so the option is still provided.
Finally, the filename of the new trajectory file is specified using the file browser. Be careful not to overwrite the original file, since the old file is still required during the modification process.
If you asked for a postscript file to be created, a filename will now be requested. You will also be prompted for the usual options for postscript files, such as color and depth-cue.
You are NOT able to change the molecule's orientation during modify trajectory, since changing the relative orientation mid-trajectory would adversely affect the postscript file and overlap options. The toolbox will close and then re-open when the modification is complete.
After the molecule has been searched, viewing a dynamics trajectory will present more options to the user. The program will ask whether all torsion values should be calculated. If so, it will ask whether the values should be saved in a data file (containing the frame number, residue name, torsion name and value). This file can later be used with other analysis tools.
Next, the user may choose to save a density plot (postscript) showing the torsion values sampled during the selected trajectory segment.
ADD TEXT:
Text labels can be placed anywhere on the MOIL-View
screen. There are two types of labels- those that are
attached to a selected atom
(and follow its movements), and those
that are in a fixed at a screen location .
Color can be
selected for each label, but currently the text size is
fixed. The size that is used in the postscript output can be
chosen, but this will not affect the size of the screen label.
This may be changed in a future version of the program.
Custom label for selected atom will allow the user to select a particle using the middle mouse button, and then enter a text line for the label.
Custom label for screen location will allow the user to type text and then move it around the screen until the desired position is determined.
Label groups of atoms allows the user to rapdily add a default label to groups of atoms chosen using a pick command. Currently, the default label includes the atom name and number. While the program does not allow the user to change this, it can easily be modified in addtext.f.
Remove one label allows the user to select a label using the middle mouse button, and then remove it.
Remove all labels will do exactly that.
Follow the on-screen prompts to obtain detailed instructions for creating/removing labels. Text labels are NOT saved in session files.
MOUSE MODE:
This menu allows you to choose what function to
perform when the left mouse button is held down and the
mouse is moved. The default function is to perform a
rotation on a 'virtual sphere' centered at the origin.
This allows for a more intuitive and accurate rotation of
the molecule than is possible using separate x, y and z
rotations from the toolbox.
Other possible choice for this function are translation, scaling or no function When translation is selected, the structure will follow the mouse pointer when the left button is held down. When scaling is selected, motion toward the center of the window will reduce the size of the structure, motion toward the edges of the window increases the size.
This mode choice can also be made directly from the toolbox, by pressing the left button over the 'R' (rotation, 'T' (translation) or 'S' (scaling) letters at the top of the toolbox. A red box will appear under the current function. Pressing the button over a letter already selected will remove the red box and return the mouse mode to 'no function'.
If the left mouse button is pressed while the cursor is over the toolbox, the toolbox function will be performed regardless of the status of the mouse mode.
The final mouse mode, Rotate bond, is only valid when the entire molecule(s) that you have loaded consists of a single uninterrupted strand. For example, water is not permitted. Before selecting this option, you should use the middle mouse button to choose four consecutively bonded atoms. Choose the rotate bond menu option, and the program will attempt to determine if rotation about this bond is permitted. If the bond is part of a ring, rotation is not allowed. If successful, the mouse will now allow rotation about the selected bond when the left button is held down. The torsion value for the four selected atoms will be updated as you perform the rotation. To stop rotating, simply change the mouse mode to another option. Remember to save the modified coordinates before exiting if you plan to use them.
This menu allows the user to adjust several parameters, such as the sphere quality level, shading and lighting of objects, and the distance criterion for the hydrogen bond option described below. Each of these choices will be described next.
Sphere quality level can be from 3 to 30, and specifies the tesselation level of the octahedron used to approximate the sphere. Higher number give better quality but slower spheres.
Hbond cutoff changes the cutoff distance for calculating hydrogen bonds. This is the distance between the hydrogen atom and the hydrogen acceptor atom. The A-H...B angle must be between 113 and 180 degrees, and is not currently user definable. Change the numbers in findhb.f if you need to change this value, and then re-compile the program.
Contact map cutoff changes the distance used to determine what is a 'contact' between two point particles. Any monomer pair with any pair of atom centers within this distance will be considered to be in contact. This means the (avg) sum of vdW radii of the particle pairs needs to be included in this distance.
Show unbonded particles allows the user to choose whether unbonded atoms should be displayed with a '+'.
Change VDW radius allows you to give a pick command to select a group of particles, then change the VDW radius for the group. This allows you to customize the sphere size to your potential function parameters. Currently these numbers are NOT saved in the session file. If you want a permanent change, modify the numbers in the subroutine 'setparam.f' and recompile the program.
Change flash rate adjust how rapidly the two molecules are interchanged when the flash feature described above is used. This may need to be adjusted to suit your tastes and machine speed.
Use shading and Use lighting simply toggle these functions, try it and see the difference.
Use z-buffer turns on and off the use of the z-buffer. The Z-buffer is what allows the machine to determine which objects are closer to the viewer than others. This buffer is essential to the proper display of space-filling objects, but on some machines (such as the Indy) there is a significant performance penalty for its use. The default z-buffer is ON with machines that support z-buffering. While important for spheres, it is not as necessary for lines, and you may decide the performance penalty of a software Z-buffer is not worthwhile. Try this option and find out.
Use fast mode determines whether spheres and cylinders are disabled while you are manipulating the molecule's orientation with the mouse. This allows you to get reasonable response time even with complicated images. If your hardware permits, turn fast mode off to redraw spheres and cylinders at each step during reorientation.
Use depth-cue determines whether depth-cueing is used. If this is selected, the object colors will appear to merge with the background color as the distance from the viewer increases. Change the behavior here if you do not like this effect.
The spheres are menu allows you to choose how spheres are displayed. Polygons creates standard filled spheres. Lines creates open spheres and can be useful to see what is within a certain distance (changing the VDW parameter) of a particle. Points creates a dot pattern for the sphere outline. Finally, opaque and transparent control whether the particle transparency (or alpha) values are used. This option only functions on those machines that support transparency. Individual alpha values for particles can be set under the color options menu. Experiment until you are satisfied with the results.
The Ball-and-stick params menu allows you to choose how the ball-and-stick and cylinder models are displayed.
Sphere scale factor changes the fraction that is multiplied with the vdW radius to obtain the ball size.
Cylinder width sets the width of the cylinders in the units of the coordinate file (usually angstroms).
Number of cylinder division sets the number of polygons used to create the cylinders (radially about the bond) and determines the cylinder quality. The ball quality is determined by the sphere quality setting.
You may combine spheres and lines by using the 'mix lines/spheres' command. A requester will ask for a 'pick' command (see below for syntax) and any particles matching your choice will be ADDED to the sphere list. Note that you cannot turn OFF individual spheres, you must turn them all off and add new ones.
Ribbons are created through the protein ribbons-add command. First you are asked to give a pick command to specify which part of the molecule will have the ribbon. See 'pick' syntax below. Next a requester will ask for the RGB color components of this ribbon. You are allowed to make different ribbons for different parts of the molecule, and they can be different colors (see color options for information on mixing RGB values to form colors). Select the 'remove' option to remove all ribbons.
While ribbons and spheres can only be drawn for molecule 1, the Ball and cylinder or Cylinder only commands will work on either molecule. If a second molecule is loaded, the program will ask which one you want to modify. Ball and cylinder draws spheres centered on the atoms, but scales the sphere radius by a user-definable parameter. Between these smaller spheres, cylinders are drawn in place of bonds. The cylinder only mode leaves out the spheres and only draws the cylinders.
Enjoy the program (bugs and all!) and please feel free to send me any suggestions, bug reports or improvements that you have made.
Carlos Simmerling, Ph.D.
University of California at San Fransisco
Department of Pharmaceutical Chemistry
Box 0446
San Fransisco, CA 94143
carlos@cgl.ucsf.edu
[3] W. Kabsch, Acta. Cryst., A34, 827 (1978).
File Read 1st Coordinates Read 1st Connectivity Write 1st Coordinates Read 2nd Coordinates Read 2nd Connectivity Write 2nd Coordinates Copy 1st to 2nd Load Session Save Session Set File Formats Coordinates CRD PDB AMBER Connectivity MOIL Bond List AMBER Trajectory DCD PATH AMBER AMBER PBC Options Show Toolbox Show Status Info Second Molecule Display Delete Flash On/Off Bond algorithm (molecule 1) Distance Connectivity Consecutive atoms Bond algorithm (molecule 2) Distance Connectivity Consecutive atoms Center object center on CM Center on selection Don't center Solvate Shell Cubic box Draw box outline Movies Generate Watch Hydrogen bonds Find Turn off Select color Video Timing Toggle default/NTSC Color Options User Defined Restore Default Backbone only No hydrogens No waters Close waters only Close residues only Transparency Pick HB color Background Color Black White Overlap Molecules Best Fit RMSD RMSD without fit Plots Postscript Drawing Normal Ball and Stick Postscript Bitmap Color B&W Trajectory 2D-RMSD Plot trajectory data Create Distance Angle Torsion Ramachandran Overlap RMSD File data Remove Distance|Angle|Torsion|Ramachandran|Overlap|RMSD|File data Save Data Distance|Angle|Torsion|Ramachandran|Overlap|RMSD|File data Save Postscript Plot Distance|Angle|Torsion|Ramachandran|Overlap|RMSD|File data Residue contact Map HH contact map Dynamics View trajectory Cluster Trajectory Modify Trajectory Torsions Load database Search Molecule Add Text Custom label for selected atom Custom label for screen location Label groups of atoms Remove one label Remove all labels Mouse Mode No function Rotation Translation Scaling Rotate bond Change Parameters Sphere quality level Hbond cutoff distance Contact map cutoff Show unbonded particles Change VDW radius Change flash rate Use shading Use lighting Use z-buffer Use depth-cue Fast mode Spheres are Polygons Lines Points Opaque Transparent Ball and Stick params Sphere scale factor Cylinder width Number of cylinder divisions Objects Are Spheres Lines Mix lines/spheres Ball and Cylinder Cylinder only Protein Ribbons Add Remove Clear All Create prep input Quit