Info Sets Editor

Description

Manage, edit, create and destroy Info Sets. Each Info Set contains information about atoms rendering (color, radius), bonding (covalent radius, max number of bonds) and residue coloring. One of those sets (Default) cannot be modified, instead it can be copied to generate other, editable, ones.

This module has no connection ports. Simply drop it in one application and use it. At the end delete it.

Info set selection

In this section you select the Info Set to edit. The Default Info Set can be edited, but the modifications are not saved (a warning message remind this).

Atom data editing

Select the element type to edit in the list. Then you can change its Covalent radius, VdW radius, maximum number of bonds (this value is disregarded in bonds computation if the Greedy bonding option is checked in the Compute Bonds module), mass and representation color.

The changes done to this and all the other sections are immediately reflected on screen if the selected Info Set here and in the Draw Structure module are the same.

Alternative bonding distance

If the Use alt. dist. option is checked in the Compute Bonds module then the bonding distance is not computed by the sum of covalent radiuses, but instead the values set in this section are used.

Here the distance is between the atom type set in the above section and the type set in this section's list.

Fragment color editing

In this section you can add/remove Fragment names from the list and edit the fragment color for the fragment name selected in the list.

Oprion file management

Here you can delete an Info Set (except the Default one) and create a new one by copying an Info Set to a new name.

The last button saves the changes into the current atom data file (see below).

Data file

The Info Set data are saved in a file read at STM4 startup. The file is searched in the following order:

  1. If the environment variable STM4_DATA is defined and points to a valid and writable file name path, this is used.
  2. Otherwise the following file is checked:
  3. Finally the file data/atom-data.dat under the STM4 installation is used.

To check which file is picked up, define the environment variable STM4_DEBUG before starting STM4.

Limitations

A button to restore the distance in the combined bonding distance to the sum of covalent radiuses is needed.

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