The Sample Composition Form
The sample composition form allows the user to enter the composition of a protein and also allows access to computed values from the composition. The amino acid composition is listed in a spread-sheet like grid array. The amino acids are listed in alphabetical order on the basis of either their 1-letter or 3-letter codes, as selected by a pair of radio buttons at the bottom of the grid. You may switch the ordering preference without losing the data.
Standard amino acid sequence files may be read from the AA Sequence section of the sample form. Amino acid sequences can be read from a text file, pasted from the Windows clipboard, or entered directly by pressing the Edit button. Sequence files may use either single-letter or 3-letter codes, but the coding must match the current selection on the Composition form. The file names for sequence files must have the extension ".SEQ" or they will not be recognized and read correctly. Spaces, numbers, punctuation, etc. will be ignored as long as they do not intervene within a 3-letter code. Thus you can paste in sequences copied from various databases that include spaces, sequence numbers, line breaks, etc.
The sequence editing form uses single-letter codes only. If you are pasting sequences copied to the clipboard, you must use the Paste command button. You should not use the Windows shortcut Paste key combination (CTRL-V or CTRL-INSERT) to directly paste into the text box holding the sequence, since this will bypass the elimination of irrelevant spaces and other potentially invalid characters. While using the editing form you can also print out the sequence. If you read in a sequence file using 3-letter codes, the single-letter sequence is generated automatically, is stored with the Sample record in the database, and becomes available for editing.
After sequence entry is complete, the total numbers of each amino acid are summed and entered into the grid array. When this is done, you are then asked whether you wish to convert cysteines into disulfides. Amino acid or conjugate composition data can also be directly manually entered into the respective grid arrays. To speed data entry, computations are not made automatically during data entry to the grid arrays, but the computations are performed when the Compute Values button is pressed or when you exit the grid arrays using the Tab key.
Sednterp can read or save composition data in special composition files with the default ending smp, which are just simple text files. This capability is primarily provided for backward compatibility with pre-release versions of Sednterp. With current versions of Sednterp it is not necessary to save composition data in such files, since the composition data is now also stored directly in the database. The Show Charge and Absorbance Data button hides the left hand section of the composition form and shows the charge at the experimental pH, the isoelectric point of the protein, the molar extinction at 280 nm, and the Absorbance per mg/ml at 280 nm. This section can be hidden and the composition grid shown again by pressing the Show AA and Conjugate Composition Data button.
Special defined denaturants affect the vbar estimates provided by Sednterp. The different equations used are dealt with in the theory section.
It is important to note that the hydration calculation depends on pH, with different values being returned for pH values <= 4. Therefore you may need to set the correct pH from the main form before you enter the Sample Composition form. After the composition is entered, the molecular weight, vbar, and hydration coefficient may be returned to the main program. If for some reason, one or more of these values is not to be used, clearing the check boxes will prevent Sednterp from using these values in further calculations. The values are returned when you use the "OK" button. The "Cancel" button will return you to the main form, undoing all changes made while the Sample Composition form was active. The "Save to Sample Database" button saves the changes and then jumps to The Saving Data in Database Form for recording this composition as a Sample record in the database. That is, the Save to Sample Database command is equivalent to pressing the OK button on the Sample Composition form and then immediately selecting Save Sample Info in Database from The File Menu on the main form.
Graphs of charge vs pH and extinction spectrum are also available. The extinction coefficients of all conjugates are not yet available in Sednterp. (Sednterp calculates extinction spectra every 2 nm over the range 250-320 nm). If computed extinction data is in doubt, the estimating database ought to be checked for which components have extinction data entered.