To open Moloc, type "moloc" in the directory you are working in (where your pdb or map files are located is often easiest).

The trick to using Moloc is to know which mouse buttons to use when. :-)

• To move through the menus, click with the RIGHT mouse button.
• To rotate the molecule, hold down the LEFT mouse button.
• To translate the molecule (along x and y axes), hold down the MIDDLE mouse button.
• To translate the molecule along the z axis (ie, through a slab), hold down the LEFT AND RIGHT mouse buttons, and move the mouse along the VERTICAL axis along the screen ("up" moves the molecule back; "down" moves the molecle forward).
• To zoom in or out on the molecule, hold down the LEFT AND RIGHT mouse buttons, and move the mouse along the HORIZONTAL axis along the screen ("left" zooms out, "right" zooms in).
• To select (or label) an atom/chain/structure, hold down CTRL while clicking on the appropriate atom with the LEFT mouse button. If you do this when no command has been specified (see "other" section of "DISPLAY Menu Info.", below), you can toggle among atom/residue labels.
• While we are talking about moving the molecule... You can change the width of the slab in the DISPLAY menu ("." or "..."): Press ":--extras for interface", then "p--set view parameters" (using the RIGHT mouse button). A bar comes up along the bottom of the window; using the LEFT mouse button, drag the yellow triangle for "slice/width" to adjust the slab width. To accept the change you've made, click in the green "accept" bar with the RIGHT mouse buton; to reset to the original value, click the red "reset" bar.

When you enter Moloc, the screen will be set up in double view (stereo).

• To change to "mono view" (2-D), press ALT- M.
• To change to "full-stereo view" (for viewing in 3D with stereo glasses), press ALT-F.

Moloc's menus are arranged in a hierarchical manner. You can direct commands by clicking on the one-letter symbols arranged along the bottom of the screen. If you click on "?", you will see short helpful descriptions of each of these one-letter commands (click "?" to toggle between descriptions on/off). You can click on these vertical one-letter symbols to direct commands, also.

• To move through the menus, click with the RIGHT mouse button on a one-letter symbol.
• "?" ("???") shows helpful short descriptions of commands
• You can exit any menu (move backwards through the hierarchy) by pressing "x--exit"
• You can get to the DISPLAY menu at any time by pressing "." or "..."
• Remember the useful ":--extras for interface" menu, available from the DISPLAY menu. Here, you can adjust the z-slab width ("p--set view parameters", increase/decrease the width of map/structure lines and font size ("m--set map, line, and font parameters"). These 2 features are especially useful when preparing a 2D view in Moloc for making poster/paper figures.

You can open a PDB file at any time from the DISPLAY menu:

1. Enter the DISPLAY menu by pressing "..." from the main menu.
2. Press "g--get entry from file"
3. Choose "p--pdb-file"
4. Press <return> to accept all pdb files in the current directory as possible choices. Or, indicated the directory where the desired pdb file is located.
5. Click the red "n" beside the file you want to open. It will change to a green "y" to indicate that you chose that file.
6. Click "x" to definitely choose that file(s).
7. Select the color that you want your model to be. (I like yellow :-) )
8. A box will come up asking what you want to name the pdb entry in Moloc. Type your desired name, and press return.
9. If you are finished opening files, then press "x--exit" to exit the "get entry from file" menu.

Now that you have opened a pdb file, you will now want to prepare it for viewing:

1. Press "e--change entry settings"
2. Click in the colored box beside the structure you want to change settings for (or press "q" to exit change entry settings menu)
3. To see the entry :-), press "z--center entry"
4. You will now notice that Moloc is in double-stereo mode; press ALT-M for mono-mode.
5. To add labels to all residues, press "l--atom labels on/off". Press this again to label only every 5 residues; press again to turn labels off.
6. To color by atom type, press "a--atom types on/off" (O=red, N=blue, S=yellow). Press again to turn this option off.
7. You can change the structure's color by "c--color entry"; you can the structure's name by "e--change entry name".
8. You can delete a structure from Moloc by "d--delete entry".
9. Press "x--exit" when you are finished manipulating the structure.

Other useful DISPLAY menu options:

• "c--center a picked atom"--click on "c"; the letter "c" will be highlighted in red along the bottom menu. Now, select the atom you want centered in the window (hold down CTRL while clicking on atom with LEFT mouse button). Turn off this option by clicking "c--center a picked atom" again.
• "t--center a typed atom"--click on "t"; the letter "t" will be highlighted in red along the bottom menu. Now, select an atom in the chain your desired atom is located in (hold down CTRL while clicking on atom with LEFT mouse button). A box will appear; type in the residue number of the residue you wish to center on. I have had trouble with this when solvent molecules are present in my pdb file with the same residue numbers as my protein residues--Moloc tends to choose the solvent molecule #100 rather than PROT #100. Go figure... Turn off this option by clicking "t--center a typed atom" again.
• "z--center visible entries"--Self-explanatory :-)
• "m--map-contour and surface visibilities"--toggle between visiblity and invisibility of electron density maps (see MAP section below)
• "a--entry activity stati"--toggle between visible ("v"--see but cannot change structure), active ("A"--see and change/edit structure; see Moloc manual), invisible (" "--makes structure invisible)

You can open an electron density map from the MAP menu. Be sure that your map is named with the proper suffix (ex, "map.pg" for mappage-formatted maps).

Last updated 2/29/00 by Cynthia Fuhrmann cynthia@msg.ucsf.edu