Draw (apple-V):

Clears the screen then draws the objects that are turned on. This just displays to the screen and does not write to the Clipboard.

Copy (apple-C):

Draws all of the objects that you have turned on to the Clipboard. E.g. Get the diagram that you like, select copy, then go to another drawing application and hit 'Paste'. If there are a lot of vectors, the clipboard may run out of memory. In these cases, write out a PICT file instead (see 'Write output file' option in the 'File' menu).

Stereo (apple-T):

The user can toggle on/off the stereo image.

Depth Cue Shading:

When this item is selected, all objects fade to whatever the background color is currently set to. If the background color option is turned off, then the objects fade to white. This option is 'toggled' off and on.

Depth Sort (SLOW):

This option sorts the vectors for Mol objects, distance lines, ED maps, and the atomic model. Albeit slow, the lines that are supposed to be in front are drawn last and do appear to be in front. This is significantly slower than normal. I suggest that you get the objects and views that you want and then hit this option just before making your final diagram or movie. While it is slow, it is worth it in the end for a high quality diagram with proper depth cueing.

Preferences...:

I put some of the more obscure menu items into a preference file such as stereo and such. The first time the program is launched, it assigns default values. Upon quitting, it writes out a preference file to the system folder. The user has the option to write out their own preference file in a separate location if they wish to. When this item is selected, the following dialog box appears...

To explain each item...

Walleyed Stereo:

When a stereo pair is drawn, it will be with a +6° rotation about the screen's Y axis. This is the 'standard' stereo pair that can be viewed with stereo glasses, or with Marty Feldman's eyes.

Cross-eye Stereo:

The stereo pair will be drawn with a -6° rotation about the Y axis. This is not the 'standard' stereo image, cannot be properly viewed with stereo glasses, but I can see easily.

Dot Color:

FRODO can simulate the surface of a molecule by placing 'dots' at a given radius about the atoms. This is done by creating a 'MOL' object and using the 'SURF' option within the MOL menu. I have tried to duplicate these colors when I read the dots in from the FRODO plot file. The carbon atoms have yellow dots about them, the oxygen's have red and the nitrogen's have blue. The default for this pop-up menu is the above 'original color scheme'. However, I thought that the user might not like this color scheme, and since these dots are in a MOL object, I allow the user to change the color scheme with this menu by selecting the 'New color' choice of this pop-up menu. If this latter menu item is selected, then all of the dot colors will be changed to the color of that particular MOL object.

Dot Size:

The size of the dots can be changed with this pop-up menu. The default size is 2 pixels in diameter. The previous selection is marked with a check mark.

Read Preference File:

Write Preference File:

As described above, all of this information (and more in the future) is stored in a file called 'MOLVIEW Preferences'. Normally it is written to and read from the System Folder without the user knowing about it. However, for machines where the System Folder is protected, or for community machines, this may not be advisable. Therefor the user may use the following 'Write Preference File' to create the MOLVIEW Preference file in another directory. Subsequently, the user can use this option to read in their own personal preference file.

Change Rot. Step Size:

The user can change the step sizes used in the 'Interactive Rotation' option to be described in the 'Misc' menu. A dialog box appears, and the user inputs the new value(s). Hit O.K. when you are done.

Bond Search #:

This option allows you to 'search' through more or less atoms when models are created. In the Read PDB, Create Mols, and Write MM file, the distance between atoms is used as the only criterea as to whether atoms are to be bonded together. I have made special dispensation for H, Mo, and Fe atoms so that proper bonds are made. The default and initial value is 30. This means that when you, for example, 'Read PDB', the 30 atoms following each atom is checked as to whether they might be in bonding distance to the first. For a protein, this value of 30 is usually sufficient. However, for AMP, for example, you need a value of ~40 since there are so many atoms within a single 'residue'. The smaller the number, the faster the program can create the objects. If you find that certain bonds are not being made as you read PDB files, Create Mol Objects, or Write MM File, try increasing this number first and then try your action again.

Set PICT Type

When I write out a PICT file, I can make its 'creator' anything that I want. If this button is clicked, then the user can force the output PICT file to be read by other graphics programs. For example, if I set the 'Creator' to be Adobe Photoshop, then a PICT file is created that has the Adobe icon. If I then 'double click' this file, Adobe Photoshop automatically launches and opens the MolView file. Be aware that some programs are better to read the PICT files than other. For example, if you do not include a CPK model, then I recommend either Canvas or MacDraw Pro since these programs will keep the lines as objects rather than converting to a bit image. If you have CPK models included, I recommend Photoshop or PixelPaint Pro.

Number of Bins for Depth Sorting:

In the option 'Depth Sort (SLOW)' in the 'Drawing' menu, the total depth (Z distance) of the objects are divided into bins. The vectors in these bins are then draw from back to front. For small diagrams, MolView will work fast and correctly with a few bins (say about 10). For larger diagrams, more bins may be needed (say 30-50). The more bins, the slower the program, but more accurate the depth perception.

Idiot Dialog boxes:

Expert Dialog boxes:

This is the beginning of further changes. This allows a naive user to not know anything and get a drawing. For now, selecting 'Idiot Dialog Boxes' allows a user to read in a PDB file and not answer any questions. I determine the number of atoms in the file and set everything else for a 'typical' conversion. Gets rid of all of the dialog boxes in this option. Will be expanding this option to the Mol creating options as well.

Refresh Always:

When this is selected, the screen is refreshed after each menu selection. This option allows a person on an LC to not have to wait so much, or a person on a Quadra to get what they want immediately.

# Slab Steps:

This allows the user to change the number of 'slices' used to slab away the structure. The more steps, the finer the slabbing routine. This is the only parameter not saved in the preference file. If this is badly set, the next user may think that something is seriously wrong with their file or MolView. Therefore, to save e-mail responses, it is not saved for the next user.

Neighbors:

Neighbor is an option found in the Geom&Movies menu. After selecting this item neighboring atoms are identified, lines drawn to them, and distances marked on the lines. This option allows you to define how this is to be done...

Font Size: Font size of the distance label on the lines

Color: Color of the lines and labels.

Min, Max distances: minimum and maximum distances defining a neighbor

Label Neighbors: Labels the atoms neighboring the selected atom.