Welcome to MolViewer 0.9
Copyright 1993  Steve Ludtke

This message will continue to appear until you 'save all' in the periodic table inspector (this saves your molecule color preferences,etc ...)

There are more than 20 new features and bug fixes in this version. I know most of you won't actually read the online documentation (you really should), but please at least read the list of new features/bug fixes in the History entry.  For those of you with old keyboards, remember, to get help, hold down ctrl-alt and click on whatever is giving you problems...

Before I start, Molviewer has a LOT of features. I've done the best I can (with limited time) to make the interface as friendly as possible, but there are still a number of places where it is easy to get confused. PLEASE USE THE ON-LINE HELP!!! It's there for a reason. If you run into something that looks like an obvious bug, you probably just don't understand what's going on. If you still can't figure it out after reading the docs, send me a message so I can fix the bug. I got a number of complaints from beta-testers "Boy, the last version was pretty buggy!". NONE of them had taken the time to send me a single bug report...  nuff said ...

The last version of MV was quite buggy. I've acutally had people beta-test this version, so hopefully it will be fairly bug free. Since its impossible to get people to read the docs, here's a few answers to questions you're likely to ask:

Q: Why don't I get a ball and stick figure in "quick" mode?
A: Because in "quick" mode, the ball and stick mode is actually a (slow) color stick diagram. It's not supposed to show a ball and stick figure. You have to use smooth mode to see the true ball and stick figures. 

Q: In SpaceFilling Quick mode I don't see anything at all. Why not ?
A: Spacefilling quick mode now supports the entire periodic table. Unfortunately, the tiff images for all of these different atoms would take nearly a meg of disk space. To avoid this, you must get molviewer to generate only those atoms you are likely to use. There is a "make quick" button on the preferences inspector. Select the atoms you want to appear in quick spacefilling mode, then press the "make quick" button. This will make pre-rendered atoms for MV to use. NOTE: You must quit and restart MolViewer before new rendered atoms will appear.

Q: Why do the atoms in quick mode seem to overlap in strange ways?
A: Quick mode doesn't do any intersection calculations. This mode is designed for getting a rapid idea of what the molecule looks like. If you want a high-quality image, use smooth mode.

Q: Why don't the spheres appear truely spherical in "Smooth" mode?
A: For speed, quick renderman renders spheres as a set of planes. It's a tradeoff. The smoother the spheres look, the longer they take to render. If you need a high quality rendering, either generate a RIB file and use /usr/prman/prman to render it photorealistically, or print the molecule. Printouts in smooth mode are also generated with the photorealistic renderer. (Printing with renderman can be confusing, so I reccomend reading the online docs before trying it...)

Q: What happened to the animation generating buttons?
A: They are now on a seperate panel, and actually work in this version. Check the Tools menu.

Q: Color doesn't seem to be working like I expect it to.
A: Did you remember to check the "use color" flag in the render control panel? Also, unfortunately I have only a monochrome NeXT, and can't check any of the color features myself. I rely on users like you to report probelms with color.

Q: My PDB proteins aren't recognized as proteins.
A: Read the docs.

Q: When I print in quick spacefilling mode I don't get a printout.
A: Quick spacefilling mode uses tiff images of the individual atoms. These images are square and are transparent past the edge of the molecule. Since the NeXT printer doesn't support transparency, printing won't work correctly. Instead, the molecule is rendered as a TIFF file, then opened with your default TIFF viewer. Printouts won't be very high quality, but at least they'll look like the screen.

Q: How much are the atoms reduced in size in ball&stick mode?
A: You can change the atom reduction factor as well as the stick size in the periodic table inspector.

Q: Large molecules seem to crash the program.
A: NOT ANY MORE THEY SHOULDN'T. Yes, that's right, I finally found a hack that gets around the bug in QRM so large molecules shouldn't crash the program. If you run into a problem with this, PLEASE send me a message and let me know.

I hope that answers some of the more obvious questions. If you have a question that isn't answered by the docs I'd be more than happy to answer it. I like to receive mail, so if you have something to say, write!  Enjoy ...
						--steve@ion.rice.edu
						  stevel@alumni.caltech.edu