Rudimentary Operating Instructions for LigEd v.1.0.1 ---------------------------------------------------- Roman Laskowski Birkbeck College, London, UK 23 Nov 1998 To run LigEd requires that you have a file called ligplot.drw in your current directory. The ligplot.drw file is generated by LIGPLOT and contains all the drawing commands from that plot, with the exception of the following:- Key to the plot The `simple residue' representation Accessibility shading LigEd is run by typing:- java LigEd This should open a frame and show the LIGPLOT drawing within it. If it doesn't, then refer to the installation instructions. The various editing options and operations are described below. 1. Menu-bar options ---------------- a. File option ----------- i. Save - Saves the current picture as a file called LigEd.drw. To ---- retrieve the current picture the next time you use LigEd, simply copy LigEd.drw over ligplot.drw prior to running LigEd. ii. Write PS file - Writes current picture as a PostScript file called ------------- LigEd.ps. You can then view the plot using any PostScript viewer, or print it on a PostScript printer. Choose whether to print in Portrait or Landscape mode. iii. Write PDB file - Writes out the coordinates of the current picture -------------- in PDB format in a file called LigEd.pdb. iv. Exit - Exits the LigEd program. Note that the current version does ---- NOT save the current picture when you exit. You must use either the "Save" or "Write PS file" options above first. b. Colours option -------------- The colour menus allow you to change the colours of the various objects on the plot. These are:- Background colour Bonds Ligand bonds Nonlig bonds H-bonds External bonds Hydrophobics Atoms Atom edges Nitrogen atoms Oxygen atoms Carbon atoms Sulphur atoms Waters Phosphorus atoms Iron atoms Other atoms Simple residues Text items Title Ligand residues Nonlig residues Waters Hydrophobics Ligand atoms Nonlig atoms H-bond lengths The colours available are as defined in your ligplot.prm file. (They are transferred to the ligplot.drw file when you run LIGPLOT). For ligand and non-ligand bonds, there is an additional colour: "ATOM_colour" which indicates that the bonds are to be coloured according to the atom-type at either end. There are a couple of additional options which alter all the colours on the plot. These are:- Black & White - which converts all colours to different greys Inverse colours - which converts the colours to a negative equivalent (which may be more suitable for making a slide, say). c. On/off option ------------- The on/off menu allows various objects on the plot to be switched on or off:- Bonds H-bonds Hydrophobics (off by default) Atoms Ligand atoms Nonlig atoms Water atoms Atom edges Text Plot title Ligand res names Nonligand res names Water names Hydrophobic res names Ligand atom names Nonligand atom names H-bond lengths d. Bonds option ------------ The bonds menu allows you to change bonds from single to double or triple, or back again. The menu-options are disabled unless a bond is currently "picked" - as indicated by a yellow cross on it (see 3c below). 2. Buttons at the bottom of the frame ---------------------------------- a. Refresh - Refreshes the image. ------- b. Recentre - Recentres and refreshes the image. -------- c. Move residue/move atom - determines whether moving or rotating ---------------------- objects on the plot affects a whole residue, or merely a single atom at a time. 3. Mouse-action in the plot area ----------------------------- a. Moving residues/atoms/text items -------------------------------- To move any of the objects on the plot click on the object with the left mouse button, drag the object to its new location and release the button. The object will be displayed in grey while being moved. Note, that to switch between moving whole residues and single atoms, use the "Move residue/move atom" button at the bottom-right of the frame (see 2c above). Note also that when you are in "Move atom" mode you will be unable to move any of the hydrophobic contact groups. You will need to revert to the "Move residue" mode to move them. When a residue or atom is moved all the related text items and bonds will move with it. Text items can be individually moved if required. b. Rotating residues/atoms ----------------------- You can rotate a residue or an atom about any atom on the plot (it does not have to be an atom belonging to the residue) by first selecting the pivotal atom. To select an atom, click on it with the right or middle mouse button. (If your mouse has only a single button, double-click instead). A green cross will appear over the selected atom. To rotate about this atom, click with the left mouse-button on any atom of the residue to be rotated and drag with the mouse while rotating. Release the button when you have reached the desired position. Whether the whole residue rotates, or only the dragged atom, depends on the setting of the "Move residue/move atom" button at the bottom-right of the frame (see 2c above). To "unselect" the pivot atom, click with the right or middle mouse button on any blank area of the plot. The green cross should disappear. Moving any text item will also "unselect" the pivot atom and clear the green cross. c. Flipping about a bond --------------------- You can flip a residue, or part or a residue, about any of its bonds. Firstly, select the bond by clicking on it with the right or middle mouse buttons. (If your mouse has only a single button, double-click instead). A yellow cross will appear over the selected bond. To flip about this bond, click with the left mouse-button on any atom on the side of the residue to be flipped. A single click will perform the flip. Clicking a second time on any of the flipped atoms will reverse the flip. While the bond is selected the menu-options on the "Bonds" menu become enabled (see 1d above). This allows you to change the bond to single, double or triple. To "unselect" the flip-bond, click with the right or middle mouse button on any blank area of the plot. The yellow cross should disappear. d. Editing text labels ------------------- You can edit any of the text labels on the plot. Firstly, select the text item by clicking on it with the right or middle mouse buttons. (If your mouse has only a single button, double-click instead). A box containing the text string will appear. You can edit the text as required. Click the OK button to accept the new version, or the Cancel button to retain the previous text label. Roman Laskowski roman@biochem.ucl.ac.uk