6) Output new 3D graphics file - Apple's *.3df file
-automatically converts CPK, B&S, and MOL objects for you.
7) Bunch of other small fixes (e.g. new picture of the kids)
June 7, 1995
1) Added a new button that controls all graphs.
a) Make Ramachandran plots
b) Make Distance plots
c) Make Edmunson wheels
d) Made hydrophobicity plots
2) Can write out pict files for all the above.
3) Re-fixed simple resource problem that prevented 'drag&drop' of
pdb files from working.
4) Title of file now appears on main window.
May 16, 1995
1) Fixed a bug in how mol objects are first made- made the pgm crash under certain conditions.
2) Created a new subroutine for making molecular surfaces using 'stipples (dots)'...
- Using all of the atoms in the atomic structure, it creates a grid of points about the atomic model.
- The user can input various 'probe' radii. e.g. a probe radii of 0.0 yields the atomic envelope, whereas a probe radii of ~1.5 is the water accessible surface area.
- This 'stipple file' is automatically written out since it is a VERY computationally intensive algorithm. BUT be aware that the envelope corresponds to the atomic model at ONLY that orientation. THEREFORE, you might what to create and then read in the stipple file BEFORE performing ANY rotations to the model.
- The 'stipple file' can be read using the 'open stipple file' option under the file' menu item.
Color options:
- Can color according to atom type
- Can color according to hydropathy: charged=red, polar=blue, hydrophobic=green glycine=yellow.
- Color according to charge: acidic=red, basic=blue, others=grey.
- Can display entire surface or only part of the surface about a particular residue.
3) You now can control the atomic bond criteria. I FINALLY made a look-up table for expected bond distances. This is now found at the end of the 'names.pdb' file and is read for all subroutines trying to make a bond. Typical input is:
C N 1.2 1.8
This means that C-N bonds are to be > 1.2 but <1.8.
4) Fixed a small display bug. Now when the screen needs to be updated, the image is created off screen and the screen is cleared the moment before the screen is refreshed. This gives the appearence that the program is faster.
5) In the Ribbon Pref. there are 3 new options.
Using the Residue Highlight option...
1) Color by charge (blue for basic and red for acidic)
2) Color as per Branden and Tooze
3) Reset all hightlights.
6) If you hold the mouse button down on while on any of the rotation buttons of the toolbox, the image will continue to rotate until you let up on the button or position the cursor off one of the six rotation buttons.
February 14, 1995
1) Changed the way windows are updated. I now store the main window image in memory. This makes window updated extremely
fast (at least 10x). This a major change because of the acceleration of the program execution.
2) The change to 1.0.4 was a change in compilers. This change screwed up some of the TEXT files. It seems that MPW sends an ASCII code of 10 for carriage returns, whereas codewarrior sends 13 for new lines. Both work in MolView, but the latter screwed up the carriage returns when reading MolView text files with other Mac programs like Word and TeachText. Forced CodeWarrior to send the proper carriage return ASCII code.
3) Tweaked the Ramachandran plot to fit within the window borders.
4) Figured out why the grow box was disappearing from some of the windows some of the time.
5) Am no longer supporting reading atomic labels in 'O' plot files. The O plot files are changing too much to bother anymore.
6) Made a subtle fix when reading PDB files and making MOL objects. Say you have two residues or molecules in nearly the same part of space. The atoms will be connected in an odd way because the atoms are so close. Not now. Bonds are only now made within each residue (according to residue number), and with residues n-1 and n+1. In this way, you can have alternative conformations of a side chain and have them all represented nearly on top of each other.
7) Fixed some of the event handling with the QuickTime movie players.
8) Fixed some error trapping when opening files (e.g. when you say cancel during a file opening, it does so cleanly now).
1) You need to rebuild your desktop after installing version 1.0.4
2) I changed compilers. When I changed compilers, several bugs were induced because of library differences. I think that I caught them all, but... Let me know if you find any. These kinds of errors take seconds to fix.
3) The new compiler should let me quickly develope an IBM-PC version by summer (I hope). Not sure how all the routines will port.
New stuff:
1) You can now adjust the slabbing step size in the 'Preference Dialog' box. This parameter is not saved since, if mis-adjusted, could make the next user think that the pgm is not working at all...
2) Created a PICT viewer. MolView can read all types of PICT files and display them in a new window. For now, the image cannot be scaled. However, if the PICT is > than the screen sized, the image is scaled to fit the screen.
3) Molview now supports System 7.5 'Drag&Drop'. In System 7.5 if you use the mouse to drag a file on top of an application, the application will force the file open and read it. MolView now does this with the following file types:
a) PICT files (any creator)
b) PDB files (any creator-TEXT format). The file name can be any length, but MUST end with .pdb, .PDB, .ent, or .ENT While this latter requirement is not theoretically necessary, I have it there to try to trap possible errors made by naive users.
c) MolView files.
d) QuickTime movies (any creator).
4) MolView will now launch itself and automatically read files that it created:
a) MolView PICT
b) MolView files
c) MolView QuickTime movies
5) Now, when reading PDB, MolView, and O plot files, a dialog box opens and shows you that it is making progress. Since this is normally done with a 1-D ribbon, thought that I'd use a 3-D ribbon...
Fixes:
1) QuickTime player in the PowerMac version fixed.
1) One can now create 3 kinds of QuickTIme movies: rotation, ribbon rainbow, and slabbing. A dialog box appears asking the user for which one is to be created.
2) Fixed a bug that limited the number of residues to be read in from a PDB file. Was causing a crash when reading in large PDB files (had temporarily fixed an array during debugging and forgot to make it dynamic).
3) Eliminated a couple of screen refreshes that slowed down execution: one extra refresh after opening a MolView file and one extra refresh after resizing the window.
1) The color palette is now stored in the preference file. Therefore, the colors you choose today will be there tomorrow when you launch the program.
2) Window positions and sizes are stored in the preference file and reference during the running of the program. For example, if you like the ribbon button window at the bottom of the screen, just drag it there and it will stay there even if you close the window and open it again later or on another day.
3) I put a trap in the program that checks to see if QuickTime is installed. If not, a dialog box opens to tell you to get it installed. I decided to not let the program run if QuickTime is not installed.
4) Improved, somewhat, the secondary structure determination. For now, check the *.struc file against the header from the PDB file and fix the *.struc file. I am currently writing a routine to do this for you as the PDB file is read in.
1) Implemented a Color Palette to control the object color rather than having to go through the color wheel all of the time. Simply now click on the color button for any object and then click on a button from the Color Palette.
2) An 'apple-click' on the Color Palette allows you to change the color of individual buttons.
3) An 'apple-click' on one of the color buttons on the Ribbon Window allows to the change the color of a residue in the ribbon diagram by opening up a window containing buttons for each residue in that segment.
4) An 'apple-click' on a colored button in the Magnified segment window will allow you to turn the highlight color off for that particular residue.
Most fixes are for PowerMac versions. The ribbon diagram and sort with others in CPK are both working just fine now.
Secondary structure prediction routine is fixed. Was having problems with water molecules at the end of the file.
Changes:
1) If MolView cannot access your System Folder, it will read and write the preference file to the directory containing your program.
2) You can not change the radii used for the CPK. At the end of the 'names.pdb' file you will see a section called 'CPK_radii'. There is a list of one letter code and atomic radii (in ) for the radii of the various types of atoms. You can now edit this.
3) Improved the icons used for files (need to rebuild desktop to see).
