6. Map-Related Features

6.1 Maps in General
6.2 Create a Map
6.3 Map Contouring
6.4 Map Extent
6.6 Map Line Width
6.7 "Dynamic" Map colouring
6.8 Difference Map Colouring
6.10 Map Sampling
6.9 Make a Difference Map
6.11 Dragged Map
6.12 Dynamic Map Sampling and Display Size
6.13 Skeletonization
6.14 Masks
6.15 Trimming
6.16 Map Transformation
6.17 Export Map

6.1 Maps in General

6.1.1 Map Reading Bug

6.2 Create a Map

From a CCP4 map use File -> Read Map. After being generated/read, the map is immediately contoured and centred on the current rotation centre.

6.2.1 Auto-read MTZ file

(set-auto-read-column-labels "2FOFCWT" "PHIWT" 0) (set-auto-read-column-labels "FOFCWT" "DELPHIWT" 1)

By default the difference map is created in auto-reading the MTZ file. If you don't want a difference map, you can use the function:

(set-auto-read-do-difference-map-too 0)

6.2.2 Reading CIF data

• (read-cif-data-with-phases-fo-alpha-calc cif-file-name) Calculate an atom map using F_obs and \alpha_calc
• (read-cif-data-with-phases-2fo-fc cif-file-name) Calculate an atom map using F_obs, F_calc and \alpha_calc
• (read-cif-data-with-phases-fo-fc cif-file-name) Calculate an difference map using F_obs, F_calc and \alpha_calc.

6.2.3 Reading PHS data

There are 2 ways to read data by scripting:

(read-phs-and-make-map-using-cell-symm phs-file-name space-group-name a b c alpha beta gamma)

(read-pdb-and-make-map-with-reso-limits imol-previous phs-file-name reso-limit-low reso-limit-high)

The first specifies the cell explicitly, and alpha, beta and gamma are specified in degrees.

The second form allows the specification of resolution limits and takes the cell and symmetry from a previous molecule (typically a pdb file).

6.3 Map Contouring

Use keyboard + or - to change the contour level if you don't have a scroll-wheel (97).

If you are creating your map from an MTZ file, you can choose to click on the "is difference map" button on the Column Label selection widget (after a data set filename has been selected) then this map will be displayed in 2 colours corresponding to + and - the map contour level.

If you read in a map and it is a difference map then there is a checkbutton to tell Coot that.

If you want to tell Coot that a map is a difference map after it has been read, use:

(set-map-is-difference-map imol)

where imol is the molecule number.

By default the change of the contour level is determined from the sigma of the map. You can change this in the map properties dialog or by using the scripting function:

(set-contour-by-sigma-step-by-mol step on/off? imol)

where

step is the difference in sigma from one level to the next (typically 0.2)

on/off? is either 0 (sigma stepping off) or 1 (sigma stepping on)

By default the map radius (98) is 10Å. The default increment to the electron density depends on whether or not this is a difference map (0.05 e^-/\AA^3 for a "2Fo-Fc" style map and 0.005 e^-/\AA^3 for a difference map). You can change these using Edit -> Map Parameters or by using the "Properties" button of a particular map in the Display Control (Display Manager) window.

6.4 Map Extent

The extent of the map can be set using the GUI (Edit -> Map Parameters -> Map Radius) or by using the scripting function, e.g.:

(set-map-radius 13.2)

6.5 Map contour "scrolling" limits

(set-stop-scroll-iso-map 0) for a 2Fo-Fc style map

(set-stop-scroll-diff-map 0) for a difference map

To set the limits to negative (e.g. -0.6) levels:

(set-stop-scroll-iso-map-level -0.6)

and similarly:

(set-stop-scroll-diff-map-level -0.6)

where the level is specified in e^-/\AA^3.

6.6 Map Line Width

(set-map-line-width 2)

The default line width is 1.

6.7 "Dynamic" Map colouring

As subsequent maps are read, they are coloured by rotation round a colour wheel. The default colour map step is 31 degrees. You can change this using:

(set-colour-map-rotation-for-map step)

6.8 Difference Map Colouring

(set-swap-difference-map-colours 1)

This option will allow the "blue is positive, red is negative" colour scheme on "Edit -> Map Colour".

6.9 Make a Difference Map

Using the "Make a Difference Map" function in the Extensions menu, one can make a difference from two arbitrary maps. The maps need not be on the same griding, or in the same group even. The resulting map will be on the same griding and space group as the "Reference" map.

6.10 Map Sampling

This value can be set by the scripting command

(set-map-sampling-rate 2.5)

6.11 Dragged Map

To change this by scripting:

(set-active-map-drag-flag 0)

6.12 Dynamic Map Sampling and Display Size

If you want to have these functions active for all maps, add the following to your initialization file 3.10.2 Scheme:

(set-dynamic-map-sampling-on) (set-dynamic-map-size-display-on)

6.13 Skeletonization

The level of the skeleton can be changed by using Edit -> Skeleton Parameters... -> Skeletonization Level... and corresponds to the electron density level in the map. By default this value is 1.2 map standard deviations. The amount of map can be changed using Edit -> Skeleton Parameters... -> Skeleton Box Radius...(104). The units are in Ångstr@"{o}ms, with 40 as the default value.

The skeleton is often recalculated as the screen centre changes - but not always since it can be an irritatingly slow calculation. If you want to force a regeneration of the displayed skeleton, simply centre on an atom (using the middle mouse button) or press the S key.

6.14 Masks

(mask-map-by-molecule imol-map imol-model invert-mask?)

If invert-mask? is 0, this will create a new map that has density only where there are no (close) coordinates. If invert-mask? is 1 then the map density values will be set to zero everywhere except close to the atoms of molecule number imol-model.

The radius of the mask around each atom is 2.0Å by default. You can change this using:

(set-map-mask-atom-radius radius)

There is a GUI interface to Map Masking under the Extensions menu.

6.14.1 Example

1. Make a pdb file the contains just the ligand and read it in to Coot - let's say it is molecule 1 and the ligand is residue 3 of chain "L".
2. Get a map that covers the ligand (e.g. from refmac). Let's say this map is molecule number 2.
3. Mask the map:

   (mask-map-by-molecule 2 1 1)

   This creates a new map. Turn the other maps off, leaving only the masked map.

To get a nice rendered image, press F8 (see Section 3.6 Raster3D output).

6.15 Trimming

(trim-molecule-by-map imol-coords imol-map density-level delete/zero-occ?)

where delete/zero-occ? is 0 to remove the atoms and 1 to set their occupancy to zero.

There is a GUI interface for this feature under the "Extensions" menu item.

6.16 Map Transformation

If you want to transform a map, you can do it thusly:

(transform-map imol rotation-matrix trans point radius)

where:

rotation-matrix is a 9-membered list of numbers for an orthogonal rotation matrix.

trans is a 3-membered list of numbers (distances in Ångst@"{o}ms).

point is a 3-membered list of numbers (centre point in Ångst@"{o}ms).

radius is a single number (also in Ångst@"{o}ms).

This applies the rotation rotation-matrix and a translation trans to a map fragment, so that when the transformation is applied the centre of the new map is at point.

Example usage:

(transform-map 2 '(1 0 0 0 1 0 0 0 1) '(0 0 1) (rotation-centre) 10)

which transforms map number 2 by a translation of 1Å along the Z axis, centred at the screen centre for 10Å around that centre.

Here's a more real-world example:

Let's say we want to tranform the density over the "B" molecule to a position over the "A" molecule. First we do a LSQ transformation to get the rotation and translation that moves the "B" coordinates over the "A" coordinates:

In the terminal output we get:

@verbatim | 0.9707, 0.2351, 0.05033| | -0.04676, 0.39, -0.9196| | -0.2358, 0.8903, 0.3896| ( -33.34, 21.14, 18.82)

The centre of the "A" molecule is at (58.456, 5.65, 11.108). So we do:

(transform-map 3 (list 0.9707 0.2351 0.05033 -0.04676 0.39 -0.9196 -0.2358 0.8903 0.3896) (list -33.34 21.14 18.82) (list 58.456 5.65 11.108) 8)

Which creates a map over the middle of the "A" molecule. Note that using a too high radius can cause overlap problems, so try with a small radius (e.g. 5.0) if the resulting map looks problematic.

Alternatively, instead of typing the whole matrix, you can use a coordinates least-squares fit to generate the matrix for you. (transform-map-using-lsq-matrix) does just that.

Heres how to use it:

(transform-map-using-lsq-matrix imol-ref ref-chain ref-resno-start ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-map about-pt radius)

Hopefully the arguments are self explanatory (ref refers to the reference molecule, of course and about-pt is a 3-number list such as is returned by (rotation-centre)).

We can now export that map, if we want.

6.17 Export Map

You can write out a map from Coot (e.g. one from NCS averaging, or masking or general transformation) using the export map function:

(export-map imol filename)

e.g.

(export-map 4 "ncs-averaged.map")