1
SEDANAL
USERS' MANUAL
Walter F. Stafford
and
Peter J. Sherwood
12 Francis Avenue
Cambridge, MA 02138
stafford@sedanal.org
sherwood@computer.org
21 May 2024
SEDANAL v7.91
[A4]
This will print as-is on A4 paper.
(8.27x 11.69-- 21.0 x 29.7 cm)
Reduce to 94% for 8.5" x 11" paper size
.
TABLE of CONTENTS
1!!!!INTRODUCTION*AND*SETUP*
1.1!!!!BACKGROUND*
1.2!!!!THE,SEDANAL,SOFTWARE,PACKAGE*
1.3!!!!INSTALLATION:,PROGRAM,AND,DATA,FILES,,PATHS*
1.3.1!!!!THE#DEFAULT#INSTALLATION:&
1.3.2!!!!ALTERNATE#INSTALLATION#METHODS&
1.3.3!!!!DEFAULT#PATH#STRUCTURE#FOR#SEDANAL&
1.3.3.1!!!!!In&summary,&for&getting&started,&the&default&directory&structure&should&look&like:&
1.3.4!!!!A#GRAPHICAL#REPRESENTATION#OF#THIS#PATH#STRUCTURE:&
2!!!!MAIN*MENU*
2.1.1!!!!PREPROCESSOR#SCREEN&
2.1.2!!!!MODELEDITOR&
2.1.3!!!!DCDT#AND#WDA#SCREENS&
2.1.4!!!!FITTER:#CONTROL#PANEL#SCREEN#AND#CONTROL#FILE#CREATION&
2.1.5!!!!BIOSPIN&
2.1.6!!!!GENERAL#PURPOSE#KINETICS#SIMULA T OR&
2.1.7!!!!NOTE:#THE#MAIN#MENU#WINDOW#CAN#PLACED#IN#THE#S C R E E N#WITH#THE #F O L L O WING#KEYBO A RD#SHORT-
CUTS:&
3!!!!MODULES*OF*SEDANAL*
3.1!!!!THE!MODELEDITOR*
3.1.1!!!!THE#NAMING#TAB&
3.1.2!!!!THE#SPECIES#TAB&
3.1.3!!!!THE#MOLECULAR#PARAMETERS#TAB&
3.1.4!!!!REACTIONS#TAB&
3.1.5!!!!MODELS&
3.1.5.1!!!!!One&Component&-&Single&Ideal&Species&Model&
3.1.5.2!!!!!One&Component&-&Two&Species&Ideal&Model&(e.g.&Monomer-dimer,&rapidly&reversible)&
3.1.5.3!!!!!Two&Component&-&Two&Species&Ideal&Model&
3.1.5.4!!!!!Three&Component&-&Three&Species&Ideal&Model&
3.1.5.5!!!!!Two&Component&-&Three&Species&Interacting&Model&
3.1.5.6!!!!!Two&Component&-&Four&Species&Interacting&Model&
3.1.5.7!!!!!Three&Component&-&Four&Species&Interacting&Model&
3.1.6!!!!MODELS#INCLUDING#NON-IDEALITY&
3.1.6.1!!!!!Hydrodynamic&Concentration&Dependence&and&Thermodynamic&Non-ideality&
3.1.6.2!!!!!Single&species&with&non-ideality&
3.1.6.3!!!!!Multiple&Species&with&Non-ideality&
3.1.6.4!!!!!Cross&Term&Non-ideality:&
3.1.6.4.1!!!!!Setting&limits&to&avoid&numerical&instability&in&the&finite&element&solutions&for&non-ideal&
systems.&
3.1.7!!!!INDEFINITE#SELF-ASSOCIATION#MODELS&
3.1.8!!!!NON-IDEAL#ISODESMIC#SYSTEM S:&
3.1.9!!!!NON-INTERACTING#SYSTEMS#OF#FIXED#KNOWN#STOICHIOMETRY&
3.1.10!!!!EDITING#MODELS#FOR#THE#SEDEQ#FITTER&
3.1.11!!!!USER#AUXILIARY#PARAMETERS#FOR#FITTING:&
3.2!!!!MAIN,MENU,-,OTHER,MODULES:*,ACCESS,BY,MAIN,MENU*
3.3!!!!PREPROCESS,ULTRACENTRIFUGE,DATA*
3.3.1!!!!LOADING#DATA&
3.3.2!!!!ADJUSTING#DATA#FOR#OFF-SETS#AND#JITTER&
3.3.3!!!!SELECTION#OF#SCANS#TO#BE#DISPLAYED.&
3.3.4!!!!SELECTION#OF#SCANS#TO#BE#FITTED.&
3.3.5!!!!PROCESSING#INTENSITY#DATA:&
3.3.5.1!!!!!Beckman&Optima&data&
3.3.6!!!!SUMMARY#OF#THE#PREPROCESSING#PROCEDURE:&
3.3.6.1!!!!Zoom.&
3.3.6.2!!!!!Interference&Data.&
3.3.6.2.1!!!!Remove&optical&jitter:&
3.3.6.2.2!!!!!Remove&integral&fringe&shifts:&
3.3.6.3!!!!!Absorbance&and&Interference&Data:&
3.3.6.4!!!!!Fluorescence&and&Intensity&(pseudo-absorbance)&data.&
3.3.6.5!!!!!Wavelength&Data&from&XL-A.&
3.3.6.6!!!!!Very&large&multi-wavelength&(MWL)&datasets&containing&several&hundred&wavelengths&-&
3.3.6.7!!!!!Deconvolution&of&Concentration&Profiles&from&Multi-Wavelength&Data&
3.3.6.8!!!!!Preprocessing&multi-speed&datasets&for&Wide&Distribution&Analysis&(WDA):&
3.3.6.9!!!!!Preprocessing&Multiwavelngth&data&from&the&Optima&
3.3.6.10!!!!!Preprocessing&Sedimentation&Equilibrium&data&
3.3.6.10.1!!!!!Testing&for&Equilibrium&
DISPLAYING,A PP R O A C H ,TO ,EQ U IL IB R IU M&
1.!!!!IF*THE*USER*HAS*ENTERED*RADII,*THOSE*ARE*USED.*
2.!!!!ELSE*IF*THE*MENISCUS*AND/OR*CELL*BASE*HAS*BEEN*CHOSEN,*IT*WILL*BE*USED*AFTER*
ADJUSTMENT*.*THE*ADJUSTMENT*IS*TO*ADD*0.02*CM*TO*THE*MENISCUS,*AND*SUBTRACT*0.002*
CM*FROM*THE*CELL*BASE.*
3.!!!!ELSE*IF*THE*RANGE*TO*FIT*HAS*BEEN*CHOSEN,*IT*WILL*BE*USED*
4.!!!!OTHERWISE,*THE*CENTER*96%*OF*THE*RANGE*OF*RADII*FOR*ALL*SCANS*WILL*BE*USED*AS*
AN*ESTIMATE.*
3.3.6.10.2!!!!Equilbrium run in standard double sector centerpiece.&
3.3.6.10.3!!!!!Multi-channel&data&with&6&channel&centerpieces&
3.4!!!!FIT,PREPROCESSED,DATA*
3.4.1!!!!THE#CONTROL#SCREEN&
3.4.1.1!!!!!Create&a&New&Control&File&
3.4.1.2!!!!!Choose&between&Analyze&Data&and&Simulate&Data&
3.4.1.3!!!!!How&to&Save&the&Control&file&if&you&haven't&started&with&the&"New"&button.&
3.4.1.4!!!!!Reload&a&previous&control&file&
3.4.1.5!!!!!Loading&cell&data&("abr")&files:&
3.4.1.6!!!!!The&control&screen&is&divided&into&several&regions.&
3.4.1.6.1!!!!!TOP&LEFT:&
3.4.1.6.2!!!!!MIDDLE-LEFT:&
3.4.1.6.3!!!!!MIDDLE-RIGHT:&
3.4.1.6.4!!!!!LOWER:&
3.4.1.7!!!!!The&Equation&Editor&
3.4.1.8!!!!!Start&the&fitting:&
3.4.1.9!!!!!Advanced&Parameters&Button&
3.4.1.9.1!!!!!Error&Estimation&Control&
3.4.1.9.2!!!!!Lamm&Equation&Solutions&(Claverie&control):&
3.4.1.9.3!!!!!Kinetic&integrator&control&
3.4.1.9.4!!!!!Fitting&Tab&
3.4.1.9.5!!!!!Plot&color&and&symbol&size&
3.4.1.9.6!!!!!Select&output&for&Simulations&
3.4.1.9.7!!!!!Set&limits&on&s&and&D&under&non-ideal&conditions.&
3.4.1.10!!!!!Concentration&dependence&of&s&and&D&without&cross&terms.&
3.4.1.11!!!!!Pressure&dependence&of&density&and&viscosity:&
3.4.1.11.1!!!!!Compressibility&
3.4.1.11.2!!!!!Pressure&dependence&of&viscosity&
3.4.1.12!!!!!Selecting&datasets&to&be&fitted:&
3.4.1.12.1!!!!!Removing&a&dataset&from&the&fit.&
3.4.1.12.2!!!!!Weighting&Factors&
3.4.1.13!!!!!Multi-Wavelength&Weighting&Factors&by&Wavelength&
3.4.1.13.1!!!!!Standard&deviation&by&wavelength&file&format&
3.4.1.14!!!!!Selecting&parameters&for&the&finite&element&solutions&to&the&Lamm&equation.&
3.4.1.15!!!!!Extinction&coefficients:&Global&fitting&with&multiple&optical&systems&-&
3.4.1.16!!!!!Local&vs.&global&parameters&-&changing&
3.4.1.17!!!!!Indefinite&Self-association&
3.4.1.17.1!!!!!Isodesmic&case:&
3.4.1.17.2!!!!!Isoenthalpic&indefinite&self-association:&
3.4.1.18!!!!!Constraining&the&range&of&parameter&values&during&fitting.&
3.4.2!!!!EXITING#THE#CONTROL#SCREEN#TO#START#FITTING&
3.4.2.1!!!!!Fitting&Screen&
3.4.2.2!!!!!Screen&Dumps&
3.4.2.2.1!!!!!Toggling&Plots&During&Fitting&
3.4.2.2.2!!!!!Displaying&the&Residuals&Bitmap&
3.4.2.3!!!!!Fitting&to&Sedimentation&Equilibrium&Data:&
3.4.2.3.1!!!!!Loading&the&dataset&-&load&equilibrium&datasets&before&choosing&the&model&
3.4.2.3.2!!!!!Choose&a&model&
3.4.2.3.3!!!!!Enter&initial&guesses&and&other&parameters&
3.4.2.3.4!!!!!Start&the&fit&
3.4.2.3.5!!!!!Global&fit&to&a&dilution&series&with&linked&cells&
3.4.2.4!!!!!Since&the&molar&masses&and&density&increments&are&known&for&the&two&components,&only&the&
loading&concentrations,&yoffsets&and&global&equilibrium&constant&were&fit.&
3.4.2.4.1!!!!!Global&fit&with&un-linked&cells&
3.4.2.5!!!!!Global&Fitting&of&Multi-wavelength&Data&