Displaying Selected NMR Models

Initially, all models are shown at once, overlayed, as thin backbone traces, colored by group, with hetero atoms, including any water present, spacefilled. This display can be restored with the [All] button.
Contents

[Model]: Displaying Individual Models

Pressing the [Model] button will display model 1. Pressing it again will display model 2, and so forth. When the model number reaches the actual number of models loaded, pressing the [Model] button again will return to 1 automatically.

It is also possible to type any model number into the model number box (just to the right of the [Model] button). After entering the number, when you click anywhere outside this box (such as on a blank white area) the specified model will be displayed.

The representation or color scheme displayed by the [Model] button can be customized.

[Water], [Hetero] Buttons

While displaying one model, but only when the "NMR Model Selection" page is visible, the [Water] and [Hetero] buttons work only on the one model selected. However, after you press [Back] to go to a different page (so the "NMR Model Selection" page is no longer visible), the [Water] and [Hetero] buttons will operate on all models.

[All]: Displaying All Models Overlayed

To display all models overlayed, press the [All] button. The representation or color scheme displayed can be customized.

Changing the Color Scheme or Representation

Press the [?] button just after the label NMR Model Script for instructions.

[Auto]: Automatic Display of Each Model

The [Auto] button shows each model, one at a time, then repeats the cycle indefinitely until the [Auto] button is pressed again. The default rendering is the same as for the [Model] button. The representation or color scheme can be customized if desired.

Always Show One Model in Black

The purpose of this option is to compare a single selected model with the other models, showing each pair in turn.

For example, enter "1" into the "Always show model" slot and then click on any blank white area outside the slot. Model 1 turns black and all other models are shown in the rainbow (group) color scheme (N terminus, C terminus).

Now press the [Model] button repeatedly to cycle through the models, one at a time. Each model is shown overlayed with model 1 for comparison.

To cancel this option, simply delete the number in the "Always show model" slot and then click on any blank white area outside the slot.

The representation, and the color scheme for all models except the black one, can be customized -- but this is tricky. See the Appendix below for details. (The presence of a model number in the Always show slot will cause any custom rendring script in the NMR Model Script box to be ignored by the [All] button, which is the initial rendering of the Always show mode. However, the [Model] button will obey the custom script, showing the Always show model in black.)

Model List

When a list of model numbers is typed into this slot, the [Model], [All], and [Auto] buttons will use this list instead of displaying every one of the models present in the PDB file. The [Model] and [Auto] buttons will follow the list in the order given, which allows models to be displayed in an order different from their numbers. Numbers in the list should be separated by commas and/or spaces. These examples are valid lists: 

  13, 7, 9, 22, 23
  13,7,9,22,23
  13 7 9 22 23
A model list can be used in conjunction with an Always show model number, which need not be a member of the list.

When the model list is deleted, the buttons will return to displaying all models present in the PDB file.

Appendix

Technical information for advanced users

The implementation of the color scheme involved in the "Always show model" option is complicated by a bug in Chime (inherited from RasMol). Therefore it is not recommended to use the "Always show model" option in combination with a custom "NMR model script". (See below for a description of this under "Group coloring bug".)

However, a similar result can be obtained by (i) blanking the "Always show model" slot, and (ii) entering a script similar to this one in the "NMR model script" box:

The above type of script assumes that you have colored the models as desired beforehand, and represented model 1 as desired beforehand. If model 1 and the current model (model=@) use different representations, the current model representation will be applied to model 1 as the [Model] button cycles through it. Therefore, you may wish to turn off the unwanted representations where indicated by the comment.

Group coloring bug and workaround

This bug arises when the group coloring scheme is applied following any select command which excludes one model, such as any of these:

Under these circumstances, the group coloring scheme fails to be applied. In order to keep one model a special color while having all other models in group color scheme, it is necessary to 'reserve' that color first, then apply the group coloring scheme to all models, then select and color the special model. Reservation of the color is necessary because otherwise the group color scheme uses all colors in Chime's limited palette, and the additional color can't be generated (error message 'unable to allocate color'). Dots are a good way to reserve a color because they can be colored independently of the atoms, and they can be turned off when no longer needed. Here is an example of the type of script which is used to keep the special model black while applying the group coloring scheme to all other models.