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Chapter 11. Menu Calculation (Alt-C)
11.1. Calculation->Recompute...
In VolSurf, the variables are automatically computed when the structures or fields are imported. However, the User can select this command to repeat the computations with different parameters.
Note: This command require the presence in the disk of the MIFs produced by VolSurf. When these fields are not present or have been deleted (option keep KONT not selected in the File->Import->Series... dialog) the command will be inactive in the menu.
The command shows the Calculation Parameters dialog:
Important: If the dialog does not appear, please check the value for Default calculation definition in the Misc preferences dialog: if set to Yes the dialog is skipped (see Preferences->Miscellaneus for more details).
In this dialog, the User can change the different parameters that control the VolSurf encoding engine pressing the three buttons shown at the right hand side of the dialog:
- Define probes
this button allows the User to define the kind of probe used to generate each molecular field. Unfortunately, GRID kont files contains no reference to the probe or probes used to generate the molecular field and the User should explicitly specify it. By default, VolSurf assumes that the first probe is Water or a polar probe. If more probes were present, VolSurf will ignore them unless the User instructs the program to use them.
Probes can be of the following types:
OH2 GRID water DRY the GRID hydrophobic probe O GRID carbonyl oxygen atom BOTH the GRID amphipathic probe O:: GRID carboxy oxygen atom N1 GRID amide NH group N:= GRID sp2 N with one lone pair N3+ GRID sp3 cationic NH3 group O- GRID anionic phenolate oxygen POLAR GRID polar probe CHARGED GRID charged probe MEP water MEP in the water probe MEP vacuum MEP in the vacuum probe Important: In VolSurf, the hydrophobic probe is handled in a very special way and requires that a water probe (OH2) was present before in the kont file.
To change the default type click with the mouse on the options menus and drag the mouse until the right option is highlighted. Individual fields can be included or excluded from the analysis clicking on use with the mouse.
When the dialog shows the desired choices, press OK. If you want to cancel your choices press the Cancel.
- Define levels
many of the variables computed in VolSurf are obtained for a certain number of cutoff levels (levels, in VolSurf terminology). Use this command to change the number of levels which will be considered in the calculations.
In this input dialog, change the number of levels clicking on the right or left arrow or enter directly the desired value in the input area in between them.
When the dialog shows the desired choices, press OK. If you want to cancel your choice press the Cancel.
- Edit levels
each probe has a predefined set of energy levels, which were selected to give the best results for a wide range of compounds. However, it is possible to edit the default levels defined for each type of probe. Please do not edit the redefined levels unless you have a good reason to do so.
This command presents first an input dialog to select the probe which will be edited. Press the button corresponding to the desired probe or Exit to go back to the interface.
Once the User press one of the buttons, a dialog like this one appears:
To change a level, click on top of it in the list and it will be copied to the Edit level input field. Edit the value and press Enter on the keyboard, the Levels list will be immediately updated.
When the dialog shows the desired choices, press the OK button. If you want to cancel the edition press the Cancel button.
Any change in the parameters is immediately reflected in the text window. When this text window shows acceptable values the User can press the OK button to start the computation or Cancel to abort it.
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