4.5 Bond Parameters

The various bond parameters can be set using the GUI dialog Draw -> Bond Parameters or via scripting functions.

The represention style of the molecule that has the active residue (if any) can be changed using the scroll wheel with Ctrl and Shift.

4.5.1 Bond Thickness

The thickness (width) of bonds of individual molecules can be changed. This can be done via the Bond Parameters dialog or the scripting interface:

(set-bond-thickness thickness imol)

where imol is the molecule number.

The default thickness is 3 pixels. The bond thickness also applies to the symmetry atoms of the molecule. The default bond thickness for new molecules can be set using:

(set-default-bond-thickness thick)

where thick is an integer.

There is no means to change the bond thickness of a residue selection within a molecule.

4.5.2 Display Hydrogens

Initially, hydrogens are displayed. They can be undisplayed using

(set-draw-hydrogens mol-no 0) ¹

where mol-no is the molecule number.

There is a GUI to control this too, under “Edit -> Bond Parameters”.

4.5.3 NCS Ghosts Coordinates

It is occasionally useful when analysing non-crystallographically related molecules to have “images” of the other related molecules appear matched onto the current coordinates. It is important to understand that these ghosts are for displaying differences of NCS-related molecules by structure superposition, not displaying neighbouring NCS related molecules. As you read in coordinates in Coot, they are checked for NCS relationships and clicking on “Edit -> Bond Parameters -> Show NCS Ghosts” -> “Yes” -> “Apply” will create “ghost” copies of them over the reference chain ².

Sometimes SSM does not provide a good (or even useful) matrix. In that case, we can specify the residue range ourselves and let the LSQ algorithm provide the matrix. A gui dialog for this operation can be found under Extensions -> NCS -> NCS Ghosts by Residue Range....

The scripting function is used like this:

(manual-ncs-ghosts imol resno-start resno-end ncs-chain-ids)

Typical usage: (manual-ncs-ghosts 0 1 10 (list "A" "B" "C"))

note that in ncs-chain-ids, the NCS master/reference chain-id goes first.

4.5.4 NCS Maps

Coot can use the relative transformations of the NCS-related molecules in a coordinates molecule to transform maps. Use Calculate -> NCS Maps... to do this (note the NCS maps only make sense in the region of the reference chain (see above).

Note also that the internal representation of the map is not transformed. If you try to export a NCS overlay map you will get an untransformed map. A transformed map only makes sense around a given point (and when using transformed maps in Coot, this reference point is changed on the fly, thus allowing map transformations on the fly). [This applies to NCS overlap maps, NCS averaged maps are transformed].

This will also create an NCS averaged map ³.

4.5.5 Using Strict NCS

Coot can use a set of strict NCS matrices to specify NCS which means that NCS-related molecules can appear like convention symmetry-related molecules.

(add-strict-ncs-matrix imol ncs-chain-id ncs-target-chain-id m11 m12 m13 m21 m22 m23 m31 m32 m33 t1 t2 t3)

where ncs-chain-id might be "B", "C" "D" (etc.) and ncs-target-chain-id is "A", i.e. the B, C, D molecules are NCS copies of the A chain.

for icosahedral symmetry the translation components t1, t2, t3 will be 0.

You need to turn on symmetry for molecule imol and set the displayed symmetry object type to "Display Near Chains".