(:title Surface from grid data:)

http://molekel.cscs.ch/wiki/uploaded/ReferenceGuide/griddata_dlg.png

Using negative and positive iso-values at the same time

Although this feature is not supported yet in the released versions, it is possible to use both negative and positive iso-values, or in general multiple iso-values, by loading multiple (one per iso-value) copies of the same molecule and then generate one surface with a different iso-value for each copy of the loaded molecule.

e.g.

It is possible to generate an iso-surface from grid data read from a Gaussian cube or ADF t41 files through the "Grid Data Surface Dialog" (Surfaces-Grid Data menu item).

To generate the surface simply press the Generate button.

Molekel 5.1.1 or newer can display surfaces generated from grid data contained in ADF Tape41 files; when grid data are read from ADF files the Grids drop-down list box contains a list of all the grids found in the file: to generate an iso-surface from a particular grid simply select the grid name in the list before pressing the Generate button. Every surface can be displayed with a different color: to change the color of a specific surface select the grid name in the Grids list view and press the Color button.

 steps with 0.01 relaxation''||

http://bioinformatics.org/molekel/uploads/ReferenceGuide/cube_surface_no_smoothing.png | Iso-surface, no smoothing http://bioinformatics.org/molekel/uploads/ReferenceGuide/cube_surface_smoothing_200_0.01.png | Iso-surface, 200 smoothing steps with 0.01 relaxation

http://bioinformatics.org/molekel/uploads/ReferenceGuide/cube_surface_no_smoothing.png | Iso-surface, no smoothing http://bioinformatics.org/molekel/uploads/ReferenceGuide/cube_surface_smoothing_200_0.01.png | Iso-surface, 200 smoothing steps with 0.01 relaxation

http://bioinformatics.org/molekel/uploads/ReferenceGuide/cube_surface_no_smoothing.png | Iso-surface, no smoothing http://bioinformatics.org/molekel/uploads/ReferenceGuide/cube_surface_smoothing_200_0.01.png | Iso-surface, 200 smoothing steps with 0.01 relaxation

Smoothing

Molekel 5.1 or newer does support smoothing of the generated isosurfaces through Laplacian smoothing.

Checking the "Real-time Update" checkbox will cause a surface to be re-generated without having to press the Generate button each time any value in the dialog box changes.

The step multiplier (dafault is 1) can be increased to decrease the resolution of the generated surface for faster surface generation.

The rendering style can be changed after the surface has been generated.

To generate the surface simply press on the Generate button.

To remove the surface press the Remove button which is enabled only if a surface has been generated.

This dialog box shows the information about the current dataset in the read-only Grid Data section.

The step (dafault is 1) can be increased to decrease the resolution of the generated surface for faster surface generation.

http://bioinformatics.org/molekel/uploads/ReferenceGuide/griddata_dlg.png

This dialog box shows the information about the current dataset in

It is possible to generate an iso-surface from grid data read from a Gaussian cube file through the "Grid Data Surface Dialog" (Surfaces-Grid Data menu item).

http://bioinformatics.org/molekel/uploads/ReferenceGuide/griddata_dlg.png

It is possible to generate an iso-surface from grid data read from a Gaussian cube file through the "Grid Data Surface Dialog" (Surfaces-Grid Data menu item).

Update in progress

Surface from grid data

It is possible to generate an iso-surface from grid data read from a Gaussian cube file by opening the through the Surfaces-Grid Data menu