The following is a list of the programs in this collection, and what they do, how to install them, and where to find the documentation. The programs installable from are Windows 9X programs written in 32 bit Delphi/Pascal. There are two hardware issues: 1. Please note that to print graphs, your printer must be local, not networked. 2. First make sure your display is set to “high color (16 bits)”, else some graphs will not show well at all. To do this: • click on “Start” at the left bottom of your screen • click on “Control Panel”, a menu item • Double click the icon labeled “Display” • Click on the tab at the top of the window labeled “Settings” • Make sure the “High color (16 bit) selection is chosen • Click “OK’ • Close the “Control Panel” window. How to load the Windows 9.x programs onto your hard drive: 1. Close down *ALL* applications, including screen savers. You must be running the Windows 9X or higher operating system. 2. Locate the subdirectory that contains the program you want to use. Download the three files from that subdirectory to your PC to c:\temp. 3. Then double-click on the “setup.exe” icon in c:\temp. The program, any sample datafiles, one DLL file, and other support files and a Word documentation file will be placed in a default directory (or in the \windows\system directory for the *.DLL supporting the ChartFX charts). You may change the name of the target directory. All the curvefitting programs have the same “look and feel,” so that once one learns the features of one, one learns them all. The curvefitting programs include a number of unique features not found in other such software. The AUC programs return association constants in molar, not optical units. Contours of the residual sum of squares surfaces may be drawn. Standard errors for parameter estimates may be computed by the bootstrap algorithm. The bootstrap estimates may be plotted as scatter plots. You have a choice of several fitting metrics. These are unique features not, to my knowledge, found elsewhere. The first group of programs is useful for analytical ultracentrifugation: 1. MwCalc: This program analyzes a single sedimentation equilibrium absorbance datafile to compute Mw and Mz molecular weight averages. The user chooses which model to use to fit the ln(C) vs. r2 data. I believe this program includes every method ever proposed for fitting ln(C) vs. r2 data. If you can think of or find another method, please e-mail me and I’ll add it in. Both cell- and pointwise averages are computed. You may save the latest computation as an ASCII disk file so that you may import the data into, e.g., Excel. This program will work with either an original XLA datafile (which contains points outside the solution column) or with a subset file, which does not contain any points outside the solution column. If you enter an original datafile, you may save the selected data as a subset file with your choice of filenames. This is a simple way of creating subset files for the other XLA curvefitting programs that currently require subset datafiles. 2. Mixedfit. This is for the simultaneous analysis of one to twelve XLA/I analytical ultracentrifuge sedimentation equilibrium absorbance or interference datafiles. This program incorporates the robust L1 metric of Lewis and O’Reilly that has been shown to be best for absorbance data. The user can select either a single ideal species, single nonideal species, ideal self-association, non-ideal self-association model, one of four ideal isodesmic models, an ideal or non-ideal dimer-hexamer isodesmic-hexamer model, or an ideal or nonideal monomer-dimer-hexamer isodesmic-hexamer model. The baseline absorbances can be floated in the curvefitting. The user needs to know the extinction coefficient of the species at the wavelengths used and the fringe factor for interference files so that one may globally fit data at different wavelengths, rotor speeds, optical systems, and loading concentrations. 3. Eqdata. This program will generate test data files for MwCalc and MixedFit. The type of system, data, noise, etc. may all be specified. Graphs of Mw, Mz, etc. may be generated and printed. This is also very useful as a general simulation program for learning about sedimentation equilibrium. 4. Heterfit: This program is for analyzing heter-associating systems. The user interface is much like mixedfit. One may include up to two fixed self association steps for both players in the hetero association. This program incorporates the robust L1 metric of Lewis and O’Reilly that has been shown to be best for absorbance data. 5. ABData: This program will generate test data files for Heterfit. The type of system, data, noise, etc., may all be specified. 6. Transfit: This program analyzes data from sedimentation velocity or approach to sedimentation equilibrium data for a single species. There are numerous choices for the sedimentation velocity situation. Up to twelve data files may be analyzed simultaneously. 7. Trandata: This program generates synthetic test data for Transfit. 8: PlnSedEq: This program allows you to rationally plan a sedimentation equilibrium experiment. You specify macromolecular parameters and the run and loading conditions, and you get a plot of the data in terms of either absorbance or fringe displacement. A very useful simulation tool. 9. StepCalc: It is possible to substantially reduce the time to reach sedimentation equilibrium using a specially made synthetic boundary cell. This program computes the amount of time saved using such a cell, and allows one to optimize the initial synthetic boundary overlay volumes. The following programs are for more general calculations: 10.Buffer: This allows you to choose from a variety of popular buffer systems, and specify either the total molarity or ionic strength, the temperature at which the buffer will be used and what temperature will be used to prepare the buffer. Then preparation directions are generated. 11. Protcalc: This program computes a wide variety of physical characteristics from the amino acid and sugar composition of a glycoprotein. For example, the partial specific volume, the refractive index increment, the 0th through 4th derivatives of the absorption spectra for your choice of three solvents, the electrophoretic mobility as a function of pH and ionic strength using your choice of two models, the titration curve at a temperature and ionic strength you specify, and the electrostatic energy of repulsion between two touching charged spherical proteins (useful in understanding how dimerization constants change with pH and ionic strength), and the conformational electrostatic free energy (useful in understanding how protein stability changes with pH and ionic strength. You may save as an ASCII diskfile the latest absorbance spectrum (or derivative) you plot. 12. CDSmooth: This program takes a Jasco CD datafile and applies Dierckx’s parameterized cubic spline method to smooth the data. In addition, the data are converted to mean residue ellipticity. This algorithm was suggested to me by Dr. Tom Laue and it is the best for the purpose, no question. 13. Aderiv: This will read in either an AVIV file or a Cary file that has first been converted by Excel as described in the documentation and will compute a 1st thru 4th derivative. 14. Seqplot: This program will read in a protein sequence of up to 200 residues and will make all sorts of conformation predictive plots. The remaining programs are nonlinear regression fits with other data: 15. DENFIT. Reads in a Jasco file of ellipticity versus temperature. Estimates Td, ΔH at Td, (and optionally ΔCp) from the data using a nonlinear regression fit with the Simplex algorithm. The user may allow either the pretransition value to be sloping, the post-transition value, or both. Paul Chun’s thermodynamic models are included. 16. DSCFIT. Reads in a DSC file (a sample is included). Estimates Td, ΔH at Td, (and optionally ΔCp) from the data using a nonlinear regression fit with the Simplex algorithm. The user has many choices of models. 17. UreaFit. This program is for fitting urea or guanidinium chloride unfolding data. The data is essentially any observable vs. molar denaturant concentration. The user has a choice of three extrapolation models. For any model the baselines are floated in the curve fit if desired according to the suggestion of Dr. Wayne Bolen. Sample datasets are *.ure and *.gdm files. 18. ITCFIT. This program takes a MicroCal ITC datafile and estimates ΔH, Ka, and related parameters from the isothermal titration calorimetry data. 19. LnKFit. Curvefits ln(K) vs T data by several different methods to estimate the underlying thermodynamic parameters. Please read these for “Hints from Heloise:” 1. Please print out and read the Word documentation file before using the software. This is extremely complex software, but I’ve tried to make it as easy to use with the most intuitive user interface I can develop. I try to error check every user entry to see if it lies within some reasonable bounds so as to prevent crashes. Some programs run to 7000 lines of code. 2. If you have an instrument (e.g., an AVIV CD), that generates datafiles that some program will not read, please e-mail me the datafile. I will then modify the software (at my leisure) and mail you a CD-ROM with the updated program. 3. If you want to move the software to another PC, move the three setup files to the new PC and run the setup program for that software. 4. All curvefit programs come with sample datafiles that are placed in the same directory as the program. Thus, you may immediately learn to use the software. 5. All the curvefit programs come with a set of configuration files ending with .CFG. The documentation explains what these do and which entries you may change. 6. The graphs generated by the ChartFX routines include palette and tool toolbars. These enable you to extensively alter the look of the graphs, the legends, and so on. One may doubleclick on a point to show the data being graphed for that point. The graphs may be very extensively modified to suit your tastes and may be exported to the Window clipboard sos you may place them in other files. I’m quite impressed with the ChartFX folks for all the neat features. 7. The programs typically list information to the memo pad in the main form. You are able to add information to this area prior to printing. For example, you may add information about the experiment that would not go into the 80 characters string most instrument software provides. You are free to change the font and font size of the memo. 8. My e-mail is holladayl@aol.com. Please feel free to contact me regarding bugs, problems, and suggestions. As soon as I get the next load of firewood split or the next bed of wildflowers set out, I’ll get back to you. 9. I have crunched biophysical chemical data (AUC, CD, UV-vis, DSC, denaturant and acid unfolding, etc) for three decades. I grew up on the Model E. I’ve written software for myself and others for three decades. I’ve written in BASIC, Fortran, APL, PL/1. I got hooked on Pascal when I bought the Turbo Pascal V2.0 compiler in the early 1980’s. I worked at Beckman on the XLA development team and wrote all the graphics code for the very first MS-DOS user interface. It was I who suggested the third party vendor for the main menu system used in the first user interface. When Delphi for Windows became available, I used V1 for the 16 bit Windows 3.x system.