Open:

This pop-up menu now directs the user as to which input file he has. After the files have been converted to a MolView file (in the case of PDB, O, FRODO, and .cart files), the structures are automatically displayed. Upon selecting this menu item with the mouse, a pop-up menu appears, and the user selects the file type...

MolView File:

All other structure files are first converted to this format and then opened. For example, I have a file called 'Fred.pdb'. The first time I look at this structure, I open it as a PDB file (see below). During the read, I am asked to save it as a 'MolView' file. Being unoriginal, I save it as 'Fred.MV'. The next day, I open 'Fred.MV' as a MolView File rather than going back to scratch with the PDB file.

PDB File:

User can open a PDB format file and create a MolView file. **Be sure that the header information is removed from the file (i.e. the first line should begin with the word 'ATOM'). Am just now getting back to fixing this bad bit of code. The user can make bond connections according to the order in which they appear in the list (Link) or according to the distance between the atoms (NoLink). In the case of NoLink, each atom is checked with the next # of atoms for whether or not a possible bond exists. The # of atoms searched through is determined by the 'bond search #' set in the preferences of the Draw menu.

If there is a chain identifier, 1000 will be added to the residue number. For example, 'A 201' becomes residue '201', whereas 'B 201' becomes '1201', and so on.

**If the file contains helix and sheet information, this routine will write out a *.PDB.struc file to be used in creating a ribbon diagram. This will probably be more accurate than the current algorithm for secondary structure determination.

Chem 3-D .cart File:

This allows the user to read in the TEXT file produced by ChemDraw 3-D called Cartesian Coordinates 1 and produce a MolView File.

O File (after version 5.9):

Alwyn Jones changed his O program such that MolView cannot read the new versions of his plot files anymore. This option can read in the new format (not the old). In this way, O plot files can do every thing that FRODO plot files can do. With atomic coordinates appended to the file, the user can finally use all the options in MOLVIEW. To use this new option, have your PDB file (corresponding to the O plot file) on the Mac. You will be prompted with a dialog box asking if you want to append a PDB file to your O plot file and where the file is to be located.

Close (_-W):

User can close this MolView File and open another. Many of the parameters are kept from the previous run of the program.

Open MOL File:

This is new with version 1.4. You can write out a separate ëMOL Fileí that will contain MOL objects (for example, this might be a C-alpha backbone of the protein that is colored blue). You can open these MOL files with this option or just drag-and-drop the MOL file icon onto the MolView icon.

Open PICT File

This will open and display a PICT file in a new window. Up to 2 PICTs can be shown in this way. You can also open these files by ëdrag-and-dropí the icon for the PICT file onto the icon for MolView..

Open Stipple File

As described above, a ëStipple fileí is a series of colored dots that represent the accessible surface of the protein. Afther MolView calculates this surface, it writes these dots to a file that can be later read by this option.

Write Output File...:

This pop-up menu directs the user to select which kind of output file they would like to write...

New MolView File:

The current coordinates are written out to a new MolView file. The coordinates saved correspond to those displayed on the screen. The new orientation and Mol objects are saved to the new MolView file. As described above, if MOL objects are not created, then the only difference between this new file and the original file may be the orientation matrix at the top of the MolView file.

PICT File (Main Window):

This option writes out the chosen objects to a file of universal PICT format. Two types of PICT files are written (transparent to the user). If space filling models (CPK) have been drawn, then the PICT file will be binary and limited to the resolution of the screen. The second type of PICT file is when there is not any CPK models displayed. This PICT file can be opened by all programs and is object oriented. This means that each line can be individually picked by other graphic programs, and the resolution is not limited by the screen.

Ramachandran PICT File:

This option writes out the Ramachandran plot to an object oriented PICT file. You must have created a Ramachandran plot first (see Geom&Movie menu).

DXF File:

DXF files are ASCII files that can be read by many 3-D CAD programs. At the moment, this option writes out a DXF file for desired C-a residues within a specified range and/or grabs a user-specified Mol object and turns it into a DXF object. We then take this file and read it into Macromodel to make very pretty 3-D rendered tubes and sheets. These models, in turn, can be made into movies with Macromind's '3-D' program. I have included a PICT file to show you an example of a rendered PICT file using this procedure.

Edmunson wheel PICT:

This option writes out the Edmunson wheel plot to an object oriented PICT file. You must have created an Edmunson wheel first (see Tool Window description).

2-D Distance Plot PICT:

This option writes out the Distance plot to an object oriented PICT file. You must have created a distance plot first (see Tool Window description).

Hydrophobicity Plot PICT:

This option writes out the Hydrophobicity plot to an object oriented PICT file. You must have created a Hydrophobicity plot first (see Tool Window description).

Apple's 3D Meta File:

NEW RENDERING TOOL. First of all, these meta files are ASCII files that are read by programs make specifically for the PowerMac (like the included 3DMF Viewer). You can create these 3DMF files on any Mac, but must go to a PowerMac to render them (make sure that QuickDraw 3D is installed on your Mac - if not, go to the Apple site - http://QuickDraw3d.apple.com) Secondly, this file will include only MOL objects, CPK, and Ball&Stick models, and ribbon models currently displayed on the screen. When writing out MOL objects, you can have the lines be very thin (Lines) or thick (cylinders). You will be asked separately for each MOL object to give a stick thickness.

(Look at the WWW page for MolView to see examples of this new file format.)