PDVIEWER FOR WINDOWS


BY

A.R. CROFTS AND H.H. ROBINSON

INTRODUCTION

The original program pdViewer was written by Howie Robinson and Antony Crofts to allow molecules with coordinates available in the format of the Brookhaven Protein Data Bank (1, 2) to be viewed on personal computers of the IBM PC family. This new version of the program has been substantially rewritten for operation under Windows 3, using the Microsoft Visual Basic programming environment.

The new program contains many enhancements, and a much more friendly user interface. All operations are menu-driven, and mouse activated. Most operations are intuitively obvious, but the program contains Help menus for most functions, which provide explicit instructions for all major operations, allowing the program to be used without a manual. The material provided here is an amplification of that in the Help functions, with some additional information about general operation, installation, the Brookhaven Protein Data Bank, ancillary files, etc.

INSTALLATION

From diskette

Change directory to your ROOT directory (C:\ if you are using the c: drive).

Place the installation diskette in the appropriate drive.

Copy pdvwin.ini to your ROOT directory (C:\).

Copy vbrun300.dll to your WINDOWS\SYSTEM directory (C:\WINDOWS\SYSTEM).

Make a sub-directory called C:\PDV on your ROOT (C:\) directory

Copy all other files (pdvwin.exe, ramachan.ex, pdvres.tpl, pdvresca.tpl, allprfls.usr, sphere.pal, pdv.ico, etc.) to C:\PDV

If you have coordinate data files in Brookhaven Protein Data Bank (PDB) format, make a sub-directory called C:\PDB

Copy all files with .ent (or .PDB) extension to C:\PDB

  • Make sure you are in the Program Group in which you want to show the program icon.
  • Click on File in the Program Manager Window
  • Click on New
  • Click on OK
  • For Windows 3.0:

    Type in a title (for example pdvWin)

    Type in program name. Name is c:\pdv\pdvwin.exe

    Click on OK.

    For Windows 3.1

    In Description box, type in a title (for example pdVWin)

    In Command Line box, type in program name. Name is c:\pdv\pdvwin.exe

    In Working Directory, type in c:\pdb

    Click on OK, till you return to Program Manager.

  • Program should be installed.
  • Double-Click on icon to run.
  • If the program fails to run, check the following:

  • 1) pdvwin.ini is in your Root directory (normally c:\)
  • 2) vbrun300.dll is in the path (normally in c:\windows\system)
  • 3) All other files are in c:\pdv
  • 4) The program may not run because it is trying to allocate more memory than you have available. This will not normally be a problem if:
  • i) You are running Windows, and you have 4 M RAM or more;
  • ii) You are running Windows for Work Groups and have more than 8 M RAM.
  • If you run out of memory, you will need to reduce the size and/or number of models (see below).

    As the program loads, it will inform you of the current size and number of models it will handle. See below about how to change these values. The program main window opens, and is automatically scaled to fill most of the width of the screen, and about 80% of the screen height. The window size can be changed to fit your preference using the standard Windows functions, and all controls will rescale automatically. If you try to make the window too small, you will lose some controls, and the program wont be usable. The window can be maximized to fill the screen by clicking the maximize arrow at top right.

    Associating structural files

    At this point, you might like to use the Associate feature under the Files Menu in File Manager to associate .PDB and .ENT files with pdvwin.exe. This will ensure that pdvWIN will run, and automatically load the file if you double-click on the item. Alternatively, you can drag the file from File Manager into a Windows Group, and then double-click the icon to load and run the program. A PDB icon is provided to replace the default icon (use Properties option under File menu in Program Manager).

    Downloading

    Updates to the program are made available on an Internet accessible server. To obtain updates:

    Use anonymous ftp to ahab.life.uiuc.edu, logon as anonymous, and use your e-mail address as a password.

  • Change directory (cd) to pub/pdvwin (type cd pub/pdvwin)
  • Set ftp file transfer mode to binary (type binary)
  • Download necessay files.
  • If you have the Winzip 5.0 program, the only file you need is pdvwin.zip (type get pdvwin.zip).

    However, there may be more up-to-date versions of parts of the package among the other (uncompressed) files.

    If you don't have Winzip 5.0 , you'll need to down-load that as well. Necessary files are in pub/winzip.

    Alternatively, copy all the uncompressed files (all files except pdvwin.zip) over to your computer (type mget *.*).

    Now print out the readme.txt file, and follow the instructions.

    FILE OPERATIONS

    General.

    File operations require two actions: First you have to get a file name, then you have to use it to input or output data. To get a file name, click on Get File Name. A file I/O window appears. You can either select an existing file by double-clicking on the filename, or type the name in the text area for a new one, and hit Enter or click on the OK button..

    INPUT FUNCTIONS

    LOADING A COORDINATE FILE

    If you have obtained this program through the University ofI Illinois Biotechnology Center, some sample co-ordinate data files will be included. The files supplied all have the extension .PDB, and are identified by a 4 character label, nxxx, rather than in the pdbnxxx.ent label used in the Brookhaven Protein Data Bank. If you are networked to a Unix machine and store other Brookhaven Protein Data Bank files there, or if you have a CD-ROM and the Brookhaven Data Bank protein sampler CD, you may find that they are in Unix format when you bring them over to your PC. The program can handle these files, but loads them a liitle more slowly than DOS format files. You can use the program unix_dos.exe to convert them to DOS format (as used by Windows programs). If you have access to Internet, you can also download files from the Brookhaven Protein Data Bank by anonymous ftp to pdb.pdb.bnl.gov.

    Brookhaven Protein Data Bank format: pdbnxxx.ent pdV format: nxxx.pdb

    To get a file name, click on Files, then on Get File Name. A file I/O window appears.

    If you have installed the program under Windows 3.1, as above, the directory menu will already be opened at c:\pdb directory. Otherwise, double click on disk and directory menus to get to the directory you want.

    You can either select an existing file by double-clicking on the filename, or type a new name in the text area, then click on OK to select. A message allows you to check that the file name is appropriate for the I/O operation.

    Models Loaded List and Status Area

    Models already loaded are listed in a drop-down list which is at the bottom of the viewing area, in the middle. If you have not loaded any models, this area will be blank. The status of loaded models is indicated by a Status Area to the right of the drop down list, or by the color of the drop-down list text after you have selected a file. Status can be Empty (white), Active (green), Inactive (red) or Visible/Inactive (blue). The Status Area has a block of color for each model, starting top left for model 0, and proceeding across the top half, then the bottom half of the area. Initially, the whole area is white (all model slots empty).

    To Input a coordinate file.

    AutoLoad method: The program will automatically load files with extensions .PDB, .ENT or .MDL. Otherwise, if you have an empty model (if the Model Status area at the bottom of the pdViewer window contains at least one white block), click on the Load button to the right of the drop-down list to load the selected file into the first available model. The model will be centered and displayed when the load is completed. If you have used up all available model slots, you cannot load a new model by clicking in the button, and the program reminds you of this. You must use the alternative method below. If you have a model loaded in one slot, and want to load a new model into a remaining empty slot, make sure you turn the loaded model Inactive (Click Active Button to change status) before initiating a new load, otherwise both models will be centered when the second load finishes. The program detects this situation before it loads a new model, and asks if you want to inactivate the currently active model(s). If you want to load two or more models, and treat them as a single coodinate data set, use the alternative loading method below.

    If you use the Associate feature under the Files Menu in File Manager to associate .PDB and .ENT files with pdvwin.exe, you can start up pdVWIN with the model automatically loaded, by double-clicking on the file of interest in File Manager.

    Manual Load method: The alternative method for loading a coordinate file gives you more control, but is less convenient. Click on Files in the main Menu Bar, then on Input File in the sub-menu. A sub-menu appears allowing you to load the data into one of any available model storage area by selecting a model number.

    Click on Load Model #. An Input Dialogue box will appear, requesting input of a model number. The new file will erase any model currently loaded in that slot.

    The file name appears in the Text area of the Models Loaded list to indicate start of load. The Status Area is updated, and text area turns GREEN to show when load is finished. Click on Center to center and display the molecule.

    When more than one model is loaded, they can be accessed, translated, viewed, etc., either separately or as a single entity. If the models are to be treated as a single entity, it is essential that you CLICK ON CENTER ONLY AFTER LOADING ALL models (with all models Active), in order to preserve relative positions of atoms.

    If all is well, skip ahead to VIEWING THE MOLECULE.

    The default configuration allows for display of 8190 atoms in each of 2 models. If the coodinate file you are loading exceeds this number, the program will inform you. The size of the models can be changed at run-time by modifying the pdvwin.ini file. The maximal model size is 32 K atoms, and the program allows only multiple models (ie. you can't have just one model). Unless you have at least 4M RAM, you might find that your computer has to swap files to disk in order to operate with large models.

    Use NotePad to edit the pdvwin.ini file.

    Find the line which starts:

    %MODELS=x, xxxxx (where x, xxxx is 2, 8190 in the default file)

    The first value is the number of models (must be 2 or more). For normal use, it is unlikely that you will want to have more than 4 models loaded simultaneously, but for building models it is sometimes convenient to be able to load many small models. The second value is the number of atoms in each model. Change the number after the comma to a new value (maximal value is 32766), and save the modified file in the ROOT directory (C:\). Note that there is a penalty for using a model size larger than the default. The program can access the larger arrays only by using a slower algorithm, so load, rotate, move, cursor and display functions are all slower. This is no great inconvenience if you have a fast machine ('486, 25 MHz or faster), but may be more noticable with slower machines. Also, unless you have at least 4 M RAM (or 8 M or you are running Windows for Work Groups), Windows may have to swap code to and from memory, slowing operation dramatically, and the computer may not be able to cope with AutoRedraw of Pictures, Rock It and Render functions (which use AutoRedraw, and need a lot of memory). Experiment with these feature till you find optimal values.

    If you anticipate changing your pdvwin.ini file often, you might find it convenient to Associate .ini files with Notepad (use Associate under File menu in File Manager), and drag the pdvwin.ini icon into the group in which pdVWIN is located. You can then edit the file by double-clicking the icon.

    TEMPLATES.

    The default settings of the program assume that the most commonly viewed files will be for protein molecules with the positions of all backbone and side-chain atoms specified in the coordinate data. The templates for drawing these residues are contained in a file, pdvres.tpl, loaded at run time. If your .PDB file loaded OK, then it was most likely in the expected format.

    For some preliminary structures, the authors make available only the coordinates of the CA-atoms. The program recognizes these CA only files, automatically loads a different template file (pdvresca.tpl), and informs you of this.

    Templates can be switched either by loading the appropriate file using the the File I/O window, or more simply by selecting from the Toggles menu.

    Click on Toggles, then on Click for CA only. If the CA only template is already loaded, this menu item will be replaced by an item Click for Full Residues, and the Togl Sidechains item will be gray to indicate that side-chain display is disabled.

    To use the File I/O method, first click on Get File Name to get template file name. For CA-only files, use pdvresca.tpl; for full amino acid structures, use pdvres.tpl. Both template files contain templates for the common nucleic acids.

    After selecting a template file, click on Input, then on Template to load the template file.

    To avoid loss of connectivity information for prosthetic groups (HETATM entries), it may be necessary to reload the .PDB file after changing template.

    VIEWING Ca-ATOMS ONLY.

    It is sometimes convenient to view only the alph-C-atoms of a protein for which all atoms are present in the file. This can be done by loading the pdvresca.tpl template file. Click on Toggles, then on Click for CA only, or use the File I/O option above. The display of the molecule is much faster, and the view is much less cluttered, but many display options (all those associated with display of side-chains) are lost.

    VIEWING NUCLEIC ACIDS.

    Both template files contain templates for the common nucleic acids (CTGAU). In order to see nucleic acid models, you need to toggle Side Chains on (see Toggles menu). If you don't want to toggle on protein side chains, but do want to see nucleic acid atoms, toggle Circle Atoms on. The atoms of the nucleic acids will be shown, but not their connectivity. Alternatively, load the pdvresca.tpl template file, so that the CA-atoms only of the protein are displayed.

    SEQINDEX

    Seqindex allows the user to import a file containing a set of values (with numerical value 0-15) for each residue in the protein sequence. The values are stored internally, and can be used to color the model (see Color by imported file below).

    The file should contain data for only one chain of one active model (proteins only), and should have one value for each residue numbered. The program asks you to select one of the active models, and to select a chain. The program assumes that the position in the file corresponds to the residue number (first entry in file is for residue 1, second is for residue 2, etc.), and assigns values accordingly. Thus, if a model has been loaded for which coordinates are given for some but not all residues, a seqindex file should contain values for all residues, and the user should check that the numbering of residues in the structural file is consistent with the known sequence, and the sequence of values in the seqindex file.

    OUTPUT FUNCTIONS

    File Picture

    This option allows you to file the display on the current screen as a .BMP file (or two files if in Stereo mode).

    First use Get File Name to select a name for the file to use.

    If you are operating in stereo pair mode (View modes StereoX or StereoW), chose a filename with less than 8 characters, because the program automatically stores two pictures, one for the left and one for the right eye, and appends L or R to the name chosen (ie. if picture.bmp was chosen as the filename, pictureL.bmp and pictureR.bmp will be stored).

    After selecting a file name, click on File Picture; a message showing the chosen name will come up to allow you to review your choice.

    OUTPUT FILE MENU

    First use Get File Name to select a name for the file to use, then click on Output Files to see a sub menu with the following options:

    PDB: Use the selected file name to store coordinates for all active models as .PDB file using current coordinates.

    Psi Phi: Make a file of phi and psi angles of a selected span of a polypeptide chain in the currently active protein model. The program ramachan.exe included with pdViewer can be used to generate a Ramachandra plot of these data.

    First use Get File Name to select a name for the file to use. Then click on Output File, then on Phi Psi Angles. The dialogue boxes will take you through selection of a chain in the currently active model, and allow you to specifiy a span of residues (click Cancel, or hit Enter to select all residues in the chain). The program will then print the information to the file named, in the following format:

    A 135 20 -46.0 -60.4

    A 141 21 -54.4 -47.0

    A 149 22 -45.5 -47.0

    A 155 23 -66.8 -43.6

    A 164 24 -61.3 -47.2

    .

    etc.

    Here, the first column gives the chain identifier (column is blank if chain identifier is not given), the second column the ATOM number of the backbone N-atom of the residue, the third column the residue number, and the last two columns the psi and phi angles.

    Coord File: Store a set of values for coordinates of all atoms shown in the current display (including van der Waals radii, and standard colors) for input to external programs. This option was originally included to allow users to generate rendered sphere images using the program sphere.exe. A more convenient display of the model in 3-D rendered spheres is now available under the View Mode Menu (see below).

    VIEWING THE MOLECULE

    If you used Autoload to load the model, it will be automatically centered and displayed when loading is finished. Otherwise, after loading model(s), click Center to center coordinates. This will automatically set scales to allow all atoms in the model to be seen using the currently selected View Mode (see below), and display the model.

    Display or Redisplay molecule

    The molecule can be viewed immediately in the current mode by clicking on Display. To select a different viewing mode, click on View Mode, and then on an option from the drop-down menu (see below).

    Normally, a single molecule is loaded into one of the model storage areas, and is viewed as a separate entity. However, there are many circumstances in which it is useful to use more than one model storage area. These including docking two molecules, building model structures, viewing a molecule too large to fit into one model, comparing molecules.

    When two models are loaded, they can be accessed, translated, viewed, etc., either separately or as a single entity. If the two models are to be treated as a single entity, it is essential that you CLICK ON CENTER ONLY AFTER LOADING BOTH models, in order to preserve relative positions of atoms.

    VIEW MODE MENU of Viewing options

    Molecules can be viewed either in mono or stereo vision. The Mono, StereoX and StereoW options allow use of color for highlighting and encoding of information about structure or sequence. These functions are somewhat limited in Stereo Red-Green mode.

    Stereo Viewing Modes:

    Red-Green and Blue-Red:

    Filters are used to select separate images for left and right eyes. Use Red filter over Right-, Green filter over Left-eye (or Red filter over left eye, Blue filter over right eye, an option used in some computer games). Suitable filters can be made from the colored transparent plastic sheets sold in art stores.

    StereoX and StereoW:

    Separate images are presented for viewing by left and right eyes.

    StereoX: Use Cross-eyed method. The left picture is for the right eye, and the right picture for the left eye. This is the easiest "unassisted" stereo-viewing method, but not everyone can get the hang of it.

    Try the following, using a simple, well defined image:

    Sit so that your eyes are about 2½ to 3 ft back from the screen. Make a frame by putting up both hands palms out vertically about 1 ft in front of you, with thumbs extended, pointing towards each other and overlapping, and forefingers about 2½ inches apart. Move this frame to and fro until you can see only the left picture with your right eye, and only the right picture with your left eye. Now open both eyes, and let your eyes relax. With practice, a single image in 3-D will form in the frame. The focus of the 3-D image appears to be in front of the screen. Further practice will allow you to dispense with the frame, when the 3-D image will appear as a third image between the two real images.

    StereoW: Use Wall-eyed method. The left picture is for the left eye, right for right. This is the orientation used in most publications, since it is appropriate for viewing with stereo viewers. To view in 3-D without a viewer, focus beyond the screen, and relax your eyes until the two images fuse into a central 3-D image.

    The default View Mode is determined by the value associated with the %VIEWMODE line in the pdvwin.ini file. Valid values are:

  • 0 = Red-Green Stereo
  • 1 = Mono
  • 2 = StereoX
  • 3 = StereoW
  • The default value is 2 (StereoX). Use Notepad to edit the file if you want to change the value. Modify the line:

  • %VIEWMODE=2
  • by changing 2 to some other value.
  • Other options in View Mode menu

    Rock It and Render options need additional memory, and may not work, or may work only by swapping to disk (clunky) if you have a limited amount of memory. With Windows 3.1, and 2 x 16000 atom models, 4 M RAM should be enough, but you may need to cut your model size down if you experience trouble. Windows for Work Groups uses more RAM, and you will need 8 M to use these options nicely.

    Rock It

    This option is a 3-D aid for the stereoscopically disadvantaged. Click on the menu item to bring up a window in which the model is "rocked" between the two stereo pair views. The option needs a stereo pair, so if you are in Mono mode, the program asks you do change. The images are first redrawn on the main display in Autoredraw mode, and the program warns you that this will take some time. Click on OK to acknowledge the message. After redraw, the images are transferred to the Rock It window, and are displayed alternately, with a frequency that can be set using the scroll bar. The rocked image provides the illusion of a partial rotation, which allows the brain to abstract 3-D features.

    Rendering:

    Render Window:

    Click on this option to bring up a window to allow generation and display of the selected atoms of the model as rendered 3-D spheres. The image generated can later be stored as a .BMP file which can be viewed, labelled, clipped, etc. using the Paint program provided with Windows.

    The Render Window has two Picture frames. Picture 1 is used to generate the image. If the AutoSave function is not selected (the default condition, AutoSave is not checked in the Screen sub-menu of the Render Window Menu Bar), the progress of image generation can be viewed in Picture 1, and a permanent version is generated in Picture 2, and can be stored to file. Do not be alarmed if the color quality in the developing image is poor. This reflects the vagaries of Visual Basic; when AutoSave is not activated, the program switches to a default palette which does not have the color range of the rendering palette. The stored picture (visible when the image is finished) has all the colors. If AutoSave is checked, the image is generated and saved in Picture 1, and can be stored to file, but only becomes visible after the image is completed. Picture 2 is not affected, so two different images can be formed. The Pictures can be viewed individually by selection of either Picture 1 or Picture 2 under the Screen menu, or they can both be viewed together by clicking Separate. This last option separates and resizes the two pictures so that both are displayed in the Render Window, with Picture 2 on the left and Picture 1 on the right. If the window size is too small, the pictures are clipped so that the central portion of each picture is displayed. If you have a display capable of showing an image bigger than the standard VGA screen (640 x 480 pixels), you should enlarge the window before clicking Separate.

    To generate a monocular view, click on Mono. The program will inform you of the current status of AutoSave in Picture 1, and ask if you want to change it. When you respond, the program proceeds with generation of the rendered image, and keeps you informed of progress.

    To generate a stereo-pair of images, click on StereoX (for crossed-eye stereo viewing) or on StereoW (for wall-eyed stereo viewing). The images are generated sequentially, and then automatically Separated to give a pair for viewing. Although the pictures are clipped, a full (640 x 480 x 256) picture is stored in each case, and both pictures can be saved individually (at full size) to file.

    To store an image, click on File BMP; an Input box appears which asks for the number of the Picture you wish to store, and a file name. Type 1 or 2, followed by a comma, and a complete path and name. The saved image will be the full size of the standard VGA screen (640 x 480 pixels). If your video card does not allow a larger screen size, you will only see a portion of the image in the program window; the full size image is always generated, and can be seen by using View Picture in the Paint program menu. The quality of the image will depend on your video card. Any card giving 256 colors at this resolution will give a nice picture, but a standard VGA card will use only 16 colors, and a poor sphere rendering.

    Hint

    The generation of a rendered sphere picture takes time roughly in proportion to the fraction of the viewing area occupied by atoms. Acceptable pictures can be obtained more rapidly by setting the frame size bigger than that required to contain the model.

    The Rock It feature in this window operates just as in the main viewing window (see above), except that the fully rendered image is rocked, and the 3-D illusion is more convincing.

    Other options:

    Set to BW: Sets the screen colors with background White, structure Black. This is useful if you want to save a .BMP file of the picture, and "decorate" it using a paint program.

    Default Colors: Resets the screen colors to default values.

    DISPLAY OR REDISPLAY OF MOLECULE

    To Display or Redisplay models, click Display, or double-click Rot, Move, Wide or Thick. These latter options are provided to facilitate redisplay after rotation, pan or zoom using the options below.

    TRANSLATION OF MOLECULE

    Rotate, Move or Zoom In or Out, and Slice

    These options use the appropriate scroll-bars at the top of the screen. In each case, the scroll-bars are used to set value. Clicking on arrows increments (or decrements) value by 1; clicking on bar increments value by 10. With cursor on slider, and mouse button down, movement of the mouse moves the slider, and changes value. The program performs the function when you click the label below the scroll-bar. Double-click to perform function and then Redisplay.

    Rotate:

    To Rotate model, first select an axis and an angle for rotation. The value appearing in the text space is in degrees. Clicking on arrows increments value by 1; clicking on bar increments value by 10. The sign of rotation is given by the right-hand rule as follows:

    With the thumb out and the hand curled, project the thumb along the positive axis. Positive rotation follows the fingers, ie. is counter clockwise. X-axis is positive to right, Y-axis is positive up, Z-axis is taken to be positive coming out of the screen.

    Offset or Move:

    To Offset or Move model, first select an axis and a displacement. The value appearing in the text space is in angstroms. Clicking on arrows increments value by 1; clicking on bar increments value by 10. Sign of displacement is positive for positive axis.

    To Move molecule (change the stored coordinates) click once on Move(X,Y or Z), or double-click to Move and Redisplay.

    To use value as a display offset, DO NOT click on Move(X,Y or Z). Coordinates are not modified, but molecule is displayed in offset position when you click on Display.

    Zoom:

    Use the Wide scroll-bar to change scale of display. The value appearing in the text space is in angstroms, and shows width of the display along the X-axis. Clicking on arrows increments value by 1; clicking on bar increments value by 10. Change in scale takes effect at next Redisplay.

    Thickness, and Slicing the Model:

    Use the Thick scroll-bar to set the thickness of the display in the Z-axis. The value appearing in the text space is in angstroms. Only atoms within this distance, centered at the zero-point in the Z-axis, are displayed. By judicious use of this function and movement in the Z-axis, slices at different depths through the molecule can be viewed.

    ACTIVATING, HIDING AND DEACTIVATING MODEL

    Models can be Active or Inactive. In the Active state, models are always displayed, and coordinates are modified by all Rotate and Move functions. In the Inactive state, the coordinates are NOT modified by Rotate or Move functions.

    Inactive models can be either Visible or Invisible. In the Visible state, the model is displayed, but the coordinates are not modified by Rotate or Move.

    These functions are useful when docking molecules, or building models.

    To toggle Active/Inactive state of model, first select the model from the drop-down list of Models Loaded, then click the Active button.

    GREEN color in text space and Status Area shows Active, RED shows Inactive.

    To make inactive model Visible (enable display), click the Visible button. RED changes to BLUE. To toggle to Invisible, click on the Visible button again. BLUE changes to RED.

    3-D CURSOR

    The 3-D cursor is the small square visible in the center of view. In normal mode, the position of the cursor is shown, in angstroms, in the text boxes at the bottom of the screen. The 3-D cursor is only functional in Stereo View Modes.

    Positioning the cursor.

    Use the mouse to place the mouse-cursor arrow at X, Y point of interest, and click left button. The 3-D cursor will move to this position. Change the cursor position along the Z-axis by moving the mouse arrow in the Y-axis, and click right button. 3-D cursor appears to move up (towards you) as the position along the Y-axis moves up.

    CURSOR MODES

    Identify mode:

    The cursor is used to identify the nearest atom. Position the cursor at point of interest, then click on Curs X, Y or Z labels at bottom of screen to find nearest atom. A message box informs you of the name and position of the atom.

    Distance mode:

    The cursor is used to find the distance between atoms. Position the cursor at the first atom, then click on Curs X, Y or Z label; position cursor at second atom , then click on Curs again. A message box informs you of the names of the atoms and the distance between them.

    Center mode:

    The cursor is positioned at the point in the molecule which will be the new zero-point in X-, Y- and Z-axes. When you click on Curs X, Y or Z, the coordinates are changed, and the molecule is redisplayed. The chosen point can either be the cursor position, or the nearest atom to the cursor

    It is often advantageous to change Wide and Thick settings AFTER positioning cursor, but BEFORE clicking to activate change. Molecule is then redisplayed at new position and new scale.

    To cursor: Center to current cursor position.

    To nearest atom: Center to atom nearest to current cursor position.

    Neighbors mode:

    The cursor is used to select an atom (the nearest atom atom to the current cursor). Position the cursor at point of interest, then click on Curs X, Y or Z labels at bottom of screen to find neighbors (as below). A message box informs you of the name and position of the atoms which match the criteria defined below.

    Program will identify either:

    H-bonds: potential H-bonding atoms, rather loosely definede as those non-C atoms between 2.5 and 3.5 Ao distance from the atom selected; or

    10 nearest non-B: ten nearest atoms non-bonded atoms (atoms which are not in the same residue as the atom selected).

    Screen text mode:

    Write text on screen at the cursor position.

    Position cursor at point, then click Curs X, Y or Z. A text input box will appear. Write text, click on O.K., and text will be displayed at 3-D position of cursor, to the right of the cursor position.

    Sub-menus enable erasure and storage of text for redisplay on screen or printer.

    Screen Only produces a temporary text entry on the screen . This is erased at next Redisplay.

    Scrn and Prntr stores the text, and redisplays it on the screen, or on the printer when model is printed.

    Clear Last Text clears last entry stored, but does not immediately effect screen display. Click on Display to show updated view.

    Clear All Text clears all stored entries. Click on Display to show updated view.

    XYZ-mode:

    The display of X, Y and Z values for the position of the 3-D cursor can be either in absolute units (with respect to the screen zero-point), or in relative units(difference between position of cursor when last cursor function was used, and present position). Values are in angstroms. Select Absolute or Difference respectively from the sub-menu. Default setting is Absolute.

    HIGHLIGHTS

    This menu sets up display effects which highlight selected features.

    HiLite Hetatoms:

    Click on this option to display prosthetic groups (HETATM entries in .PDB file) in HiLite Hetatom color.

    To change colors of display, use Screen Colors under Parameters Menu

    Select residues:

    Click to see sub-menu, then click By Residue Number, or By Residue Type.

    Residues can be selected either by residue number, or by residue type. If the molecule contains more than one polypeptide chain, the residue number is ambiguous, and the program will request that you select a chain identifier. Select the chain in which the residue of interest is found; a list of identifiers is provided in the pop-up dialogue box which comes up when you click on Chain ID.

    Selection by number can be by individual residue (type in residue number), several residues (type in residue numbers, separated by commas, e.g. 24,36,37,98,103), or by span (type start and end residues separated by hyphen, e.g. 37-46). To terminate selection, type Enter or click OK.

    For selected residues, the side-chain is always displayed (except when the CA-only template is used), independently of the selection of the Toggle parameters for side-chains and backbone (see Toggles).

    For each residue, select is a toggle function, so individual residues can be deselected by selecting a second time.

    Residues selected by number are displayed in the Render Window images. Residues selected by type are not displayed in the Rendered images.

    HiLite Selctd Res:

    Click on this option to display selected residues in HiLite Residue color.

    Line Width:

    The default linewidth for drawing bonds is 1. To change line width used in the display and printer output, click on Line Width, and select a new value.

    Color Atoms:

    Click on this option to displays color coded circles for atoms in selected items (selected residues, or Hetatoms if HiLited).

    Atom colors are:

    C-grey; O-red; N-blue; H-white; P-purple; S-yellow; Mg-green; Zn-brown; Fe-red; Cu-blue; Co-purple; Mn-green, Mo-brown.

    Number Selctd Res:

    Click on this option to display the single letter code and number for selected residues. The number is positioned 0.5 A to right of CA atom. Takes effect on next, and all subsequent, Redisplay, until selected residue(s) are deselected, or the option is toggled off.

    Clear Selctd Res:

    Click on this option to deselect all previously selected residues.

    Coloring On/Off

    Click on this option to change coloring mode for model Display or Rendering. When Coloring On is indicated, the model will be colored according to either Sequence Index (see Profiles menu) or the coloring selected using the Coloring Tools in the PDB Information window, depending on which was last used. Click on option to change to Coloring Off. In this mode, coloring is according to options selected under the HighLights menu (Display) or according to atom type (in Render Window).

    Other hilighting options:

    3-D Rendered Spheres: See Render Window under View Mode Menu.

    Coloring by Index Parameter: See the options under Profiles Menu.

    Coloring of sequence and prosthetic groups: See PDB Information under Options menu.

    OPTIONS MENU

    PDB Information:

    This option brings up a window to allow you to:

  • 1) View the information found in standard-format PDB (.ent) files as a preamble to the coordinate data.
  • 2) View a structural cartoon generated by the program, representing the information on features of secondary structure contained in the preamble.
  • 3) Color the model by sequence span. A span can be of any length, from a single residue to the entire model. Up to seven chains per model can be handled. Chains are colored separately, but all coloring information is stored, and displayed on next Display or Render.
  • 4) Color the Hetatoms. Each prosthetic group separately identified can by colored individually.
  • The PDB Information window has three main areas: i) the Menu bar at the top; ii) a set of Coloring tools below the Menu bar; iii) a Text area which accounts for most of the window area. The first and last of these are self explanatory. The Coloring tools are described more fully below.
  • Read File

    When the window appears, first click on Read File to read-in the information in the file (the non-coodinate information contained in a preamble to the coordinates in most files). The program will reopen the PDB file of the active model(s), decode and load the following information:

  • a) If available, sequence information is loaded, and the chain identifiers found are loaded into the drop-down list labelled Chains.
  • b) The Hetatoms (prosthetic groups) found are loaded into the drop-down list labelled Hetatoms.
  • c) If the file contains structural information, a Structural Cartoon is generated showing the secondary structure of the first chain found. This is displayed in the top of the four sequence information rows. The cartoon shows Helix (structural code H) - yellow, widest band; Turn (structural code T) - purple, next widest band; Sheet (structural code E for extended chain) - red, next widest; Coil (structural code C) - blue, thinest band. Secondary structure for all chains is recorded, and can be examined by clicking on the chain identifier in the drop-down list.
  • d) If the file contains sequence information, the sequence (in single-letter code) is displayed in the next row. The span displayed can be selected by clicking on the Cartoon.
  • e) Below the sequence is the secondary structure in single-letter structural code (HETC). The structure is aligned with the sequence, and changes with it. If no structural information is contained in the file, all residues are assumed to be in random coil configuration ©.
  • f) The fourth row (initially set to all zero) displays the numerical color code set for the sequence. The numbers correspond to the palette displayed below, from 0 - gray, on the left, to 7 - red on the right. The numbers will change after selection of a color, and will remain aligned with the sequence.
  • Coloring

    The model can be colored by sequence span using four tools, available under the Coloring Menu.

    Color All: First select a color by clicking in the palette, then click on Color All to color all residues in the currently selected chain.

    Start Residue, End Residue: A span can be selected and colored by clicking on the Cartoon to select a starting residue for the span, and then on Start Residue. Next click on the palette to select a color, then click back on the Cartoon to select an end residue for the span, then on End Residue to complete the selection and coloring.

    Coloring Tools Scroll Bar and Sequence Info Text Box: Start and End residues of a span can be selected more precisely using the Scroll Bar and Cartoon together. When you click on the Cartoon, the nearest residue to the right of the point clicked is selected, and residue number, residue type, residue structure and current residue color are recorded, and displayed in the Sequence Info Text Box. The residue displayed can be changed by clicking on the arrows of the scroll bar (change by 1 residue), or on the bar itself (change by one tenth of the sequence length) or by sliding the scroll bar slider (with mouse pointer on slider, hold down left mouse button, and move slider using mouse. Bar is sequence length). First selected start residue and click Start Residue, then select a color, then select end residue and click End Residue to complete color-coding of span selected.

    Select Text: A span can also be selected from either the sequence or structure text box by using the mouse to highlight a span. First select a color by clicking on the palette. Then select a span,- position mouse pointer at start; with mouse left-button held down, drag pointer to end residue and release. Selected text will be highlighted. Then click on Select Text. Color code will change to reflect selected color.

    Coloring Hetatoms

    To color a Hetatom (prosthetic group): Select color by clicking on palette, then click on down arrow of Drop-down List to show list, then click on Hetatom to select. The color selected will be appended to the Hetatom name in the list (and text box).

    If coloring of Hetatoms doesn't work, it is probably because the HET lines in the file preamble contain a different number for the Hetatom than the residue number in the HETATM lines. You can use a text processor to fix this, but will have to read in the file again before the editing takes effect.

    Show Text

    Display text from informational preamble of PDB file. All lines before the coordinates (ATOM) lines are displayed. Text can be selected and cut to the ClipBoard using the mouse and standard Windows procedures.

    Save Model

    You can save the information about sequence and structure in the protein chains as Model files, which can be read by pSAAM. This is useful if you want to test the prediction and sequence exploration algorithms of pSAAM against a known structure. Click on Save Model in the Menu bar, and the program will suggest a file name. The name will be that of the input file, but with the extension .mod. If the molecule has more than one chain, the Chain Identifier selected (and displayed) in the Chains drop-down list will be appended to the file name before the extension. If you don't like the name suggested, the program offers you the chance to type in a name of your choice, or to abort the operation.

    Help

    Show the Help text for this window.

    Quit

    Quit this window, and return to Display window.

    Screen Colors:

    This option allows you to change many of the default Screen Colors. On clicking the menu item, two drop-down menus are provided to allow you to select particular items. First selected option from the options menu, then select color from color menu. Options available allow you to change Background Color, Residue Color, Color of HiLited Residues, Hetatom Color, and Color of HiLited Hetatoms.

    Plot options:

    On clicking the menu item, a drop-down menu appears to allow selection from the following options:

    Output to ->:

    Click on this option to bring up a second drop-down menu of output options. The default option is Printer in Portrait mode.

    Click on Printer (Portrt) or Printer (Lndscp) to redirect output to Printer (in Portrait or Landscape Mode respectively; the current Windows printer is used). Set printer mode (Portrait or Landscape) before starting pdViewer program. Click on Printers icon in Control Panel Window, and select SetUp to change mode.

    Click on File to store plot data in HPGL format for later output to an HPGL Plotter or other device. Various settings for scale, pencolors, etc. can be changed by selection from other options in this drop-down menu. The program will ask for a filename when you select a plot mode from the Plot menu.

    Plot Scale:

    Use to set scale of printer or plotter.

    Remaining options enable various plotter functions to be set before output to File.

    Autoredraw:

    Toggle to enable automatic redraw of graphics when pdViewer Window is pushed, obscured or minimized. If this function is not enabled, the picture in the display window is lost, but can be restored by clicking on Display, etc. When the model being viewed is relatively small, redisplay is more convenient. However, for large models, setting Autrodraw on may save time if your application requires switching between pdViewer and another window.

    Recorder:

    Activates the Windows Recorder. See Recorder Help or Windows manual for instructions. The Recorder can be used to store the key-strokes, mouse activity, etc., used in loading or orienting a structure, or a stored Recorder file can be replayed to quickly get to a previous orientation. This is a useful option for demonstrations, lessons, etc., especially if the full utility of the nested macros available using Recorder are exploited. The program checks to see if the Recorder is already running. If not, the program starts up Recorder. If it is running, the program asks you to check the the current title. The title is the text in the Title Bar of the Recorder window. When first activated the title is "Recorder - (Untitled)". The title will only change if you elect to open a recorder file, or save the current tape. You can check the title by using Alt Tab to cycle through the active applications. The program needs to know the correct title so as to be able to pop up the icon, close the application, distinguish between multiple recorders, etc. If the program can't find a Recorder under the current title, it will ask you to check the title until it does find one.

    IMPORTANT. You must run a recorder file with all window parameters the same as when the file was recorded, including the position of files in directories. This is because the mouse actions are recorded with respect to the Screen coordinates.

    PROFILES MENU

    This menu provides access to several options which make it possible to color the model according to residue type, or local physico-chemical environment.

    Select Palette

    Several color palettes are provided, and can be selected by clicking on Select Palette.

    Palette 1 - 5. The first five palettes are generated by using a continuous gradient between two colors, with an admixture of a third in some palettes. In future, these will allow graded coloration, but the present inadequacies of Visual Basic's color option allows only a few colors to be displayed.

    QB colors are the sixteen colors available in Quick Basic, which are accessible under Visual Basic. These are arranged (roughly) in increasing order of "brightness".

    Sph. colrs are the colors used in generation of shaded sphere pictures. Although only one shade for each of eight colors is displayable under Visual Basic, the spheres are rendered using 128 shades. Use this palette to preview colors if you want to produce a .BMP output file (see under Render option). The palette is arranged in rainbow order (black/grey, purple, blue, light blue, green, yellow, orange/brown, red).

    Select Index

    At run-time, a set of indices are preloaded from the file allprfls.usr provided with the package. Each index has 20 values, one for each of the 20 common amino acid residues. Indices provided include many commonly used hydropathy indices, the secondary structure preferences indices for soluble proteins of Chou and Fasman, and similar indices for membrane proteins from Rao and Argos, and a set of secondary structure preferences indices for a richer set of structures derived from the work of Laura Walsh and Antony Crofts (unpublished). The maximal number of entries in the file is 20 indices, all presently used. Users can modify the allprfls.usr file by deleting an existing index, and adding another (see modifying allprfls.usr in Appendix)

    Color by Index:

    Structure will be color-coded according to the normalized value (on a scale 0-15) of each residue in the current selected index, so that the color of each residue corresponds to the color at that position in the palette selected (from 0 at right to 15 at left).

    Color by SeqIndex:

    Profiles (mean value in span), and amphipathy profiles, calculated as below, are stored internally, and values are used to color-code structure by selection of Color by SeqIndex. Structure will be color-coded according to the value for each residue in the stored sequence profile.

    Calc Profile:

    Calculates a profile using a running average over 7 (default value,- can be changed by using Change Params. option) residues using the selected index. Profiles are smoothed using 2 cycles and a span of 5 (default values,- can be changed using Change Params. option), and values are normalized to scale 0 - 15. First select an Index, then click on Calc Profile, then click on Color by SeqIndex. Select a palette from the drop-down menu, then click Display. The color of the residue corresponds to the normalized value (on the scale 0-15) in the profile generated using the index selected, as indicated by the position in the palette displayed, with 0 on the left and 15 on the right.

    Calc Amphi:

    Calculates an amphipathy profile at the helical (100 deg.,- default value) or sheet repeat (170 deg.,- use Change Params. option to set angle parameter for this or other repeats), using the selected index and a span (default span is 7). Profiles are smoothed using 2 cycles and a span of 5 (defaults, or use values entered using Change Params. option). Profile values are normalized to scale 0 - 15. First select an Index, then click on Calc Amphi, then click on Color by SeqIndex. Select a palette from the drop-down menu, then click Display. The color of the residue corresponds to the normalized value calculated (see above).

    Color by imported file:

    Sequence index can be set by calculation (as above), or by importing a file of values (see File Menu/Input/SeqIndex above). To use the imported sequence index, click on Use Imported. To disable, use Select Index option.

    When the Use Imported option is selected, the temporary array used for setting the color palette in Color by SeqIndex mode is set using the imported sequence index values. The imported values will be appropriate for only one chain, in only one model, and values will be be set only for the chain selected. The values can then be viewed by selecting Color by SeqIndex, then Display. Calc Amphi and Calc Profile routines change the values in the temporary array, but will use the imported sequence index for calculations as long as the option has not been disabled. However, after a calculation, the display will reflect the calculated values, not the sequence index values imported. To regenerate the coloring by sequence index value, click on Use Imported again.

    Change Params:

    To change span, angle for amphipathy calculation, and smoothing parameters, click on this option, and enter new values in the pop-up dialogue box.

    TOGGLES MENU

    Togl Sidechains:

    Toggle display of amino acid side-chains. The default (initial setting) is off, so only protein backbone atoms are displayed initially.

    Nucleic acid bonds will only be visible if side-chains are toggled on.

    Togl Backbone:

    Toggle display of backbone atoms. Initially on (item is checked, and backbone is displayed). When toggled off, backbone atoms are not displayed, except for the Ca-atom of any selected or highlighted residues. Side-chain atoms of selected residues are displayed. If side-chains are toggled on, the side-chain atoms are displayed (except the Ca-atom). These display options are carried over into the Render Window. Note however that only side-chains selected by number (not those selected by type) will be displayed in the Render Window.

    Click for CA only / Full Residues

    Toggles between templates for display of Ca-atoms only, or full residues. The appropriate template file is loaded, and used for all displays. Because of the reduced drawing when Ca-only models are selected, the display is much faster. This can be handy when orienting large models. Initially, Full Resdues are selected (and "Click for CA only" appears in the menu), unless the file loaded has only Ca atoms, in which case the Ca templete is loaded.

    Togl Hbonds:

    Toggle display of H-bonds recorded in .PDB file. Initially off.

    Togl Water:

    Toggle display of O-atom of water molecules in .PDB file. Initially off.

    Circle Atoms:

    Toggle display of circles at each atom of main molecule. Initially off. Circles are useful for seeing atom type, and display faster than the filled colored circles available under High Lights/Color Atoms.

    Circle HetAtoms:

    Toggle display of circles at each prosthetic group atom. Initially off. Circles are useful for seeing atom type, and display faster than colored circles (High Lights/Color Atoms).

    PLOTS

    The Plots menu allows selection of plot options corresponding to the View Mode options. What happens when you select a mode depends on the Plotter Output Option selected (see above). The default option is Printer in Portrait mode.

    Printer

    If one of the Printer options has been selected, the program sends the data to the Windows printer. All toggles, text and highlights in the current display are recognized, and produced in the printed picture.

    File

    If the File option has been selected, the program asks for a file name, and then writes text to the file, in Hewlett Packard Graphics Language (HPGL), of the commands needed to draw the structure. All options selected from the Toggles Menu are recognized, but some items from the HightLights menu,- Color Circles, Number Atoms,- and Text generated using the cursor Text option, are not. The scaling and pen selection options used are those selected from the Parameters Plot Opions drop-down menu. The default values generate plots suitable for standard 8.5" x 11" paper on a plotter in landscape mode. HP Laserjet III printers should be set to Landscape and HPGL modes before attempting to plot data filed under this option.

    APPENDIX

    Modifying the ALLPRFLS.USR file

    In order to accomodate the plethora of prediction and hydropathy indices in the literat-ure, and the requirements of individual users, the program reads in a file of indices for calcul-ating profiles. A total of 20 user profiles can be included. The present ALLPRFLS.USR file contains an assortment of indices for hydropathy and prediction, which should serve most purposes. However, the user is free to add indices, and the information in this section should make this straightforward. Since the present file already has 20 profiles, it will be necessary to replace an existing index.

    In order to add new indices, use a text editor to modify the file ALLPRFLS.USR, and note the following rules:

    line 1: The first line in the file is the number of profiles. To add a profile, change this number by adding one. The maximal number is 20; to add a profile when the file contains 20, delete an existing profile.

    The profiles are stored in the following format, where n is 1 if this is the first profile, or otherwise the last line of the previous profile:

    line n+1: The name of the profile, as you would like to see it displayed, in standard

    ASCII characters, with a <CR, LF> to terminate.

    lines (n+2)-(n+21): The index value for each amino acid. The values must correspond to the

    order of amino acids below:

    A E Q D N L G K S V R T P I M F Y C W H

    Each value must be on a separate line, ie. is terminated by <CR, LF>.

    line n+22: The name of the following profile.

    line (n+23)-(n+42): Index values for the profile.

    etc.

    After changing the value in the first line, move the cursor to the line immediately

    below the last item in the file, and add the name of your new profile, <Enter>, then the 20 index values in the order shown above, with <Enter> to terminate each value. Check that you have added 21 new lines.

    Notes on some hydropathy indices included in ALLPRFLS.USR

    The values for the Eisenberg Consensus Hydropathy (3) have been multiplied by 3 to bring them into a range similar to those of other indices scaled in free-energy (kcal/mol) units. Routines using this index are appropriately modified.

    The Rao and Argos Membrane Helix Parameter (4) is included in two formats,- the

    original set scaled to probability, and a set scaled to a range similar to as to those of other

    hydropathy indices scaled in free-energy (kcal/mol) units.

    Indices with names in capital letters are taken from the review by Cornette et al. (5).

    Structural Propensity Indices.

    A set of indices has been included in the ALLPRFLS.USR file which are probability

    parameters of the type calculated by Chou and Fasman (6), but using a new classification of the structural data base (Laura Walsh and Antony Crofts, in preparation). The new classification has taken account of the fact that buried structures are different in composition from surface structures.

    Seqindex Input Files

    The format of seqindex import files is the simplest possible,- one value for each residue, starting with the first. The program uses the residue number from the PDB input file as a pointer into this array of values, ie.the residue 5 will be colored using the fifth value, etc. If you want to color only a few residues, or spans of the sequence, the coloring tools in the Pdbinfo window are more useful.

    REFERENCES

    1. 1) Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) "The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures". J. Mol. Biol. 112, 535-542
    2. 2) Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F. and Weng, J. (1987) "Protein Data Bank" in Crystallographic Databases - Information Content, Software Systems, Scientific
    3. Applications, (Allen, F.H., Bergerhoff, G. and Sievers, R., eds.), pp. 107-132. Data Commission of the International Union of Crystallography, Bonn/Cambridge/Chester
    4. 3). Eisenberg, D. (1984) Ann. Rev. Biochem. 53, 595-523
    5. 4). Rao, J.K. and Argos, P. (1986) Biochim. Biophys. Acta, 869, 197-214.
    6. 5) Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and DeLisi, C.
    7. (1987) J. Mol. Biol. 195, 659-685
    8. 6). Chou, P.Y. and Fasman, G.D. (1978) Adv. in Enzymology, 47, 45-148.