EVAL reciprocal lattice map

It is possible to map all the pixels from a set of images to a reciprocal lattice map. No a-priori knowledge of the lattice is needed for this transformation.
This page describes the procedure to create these maps and how to inspect them in coot.

From image to reciprocal lattice

The program img2r creates a 3-dimensional reciprocal lattice map. This map is defined in the laboratory system ( x points the xray source, z points up (zenith) and y makes a right handed system). Every item in this map corresponds to a pixel in reciprocal space.
The minimum set of commands for img2r are: Example:
thmax 15
maxdim 100
read *.sfrm
contour recip

This will create:

Convert reciprocal lattice to CCP4 density map

The cntfile from the previous chapter can be converted to a CCP4 density map with cnt2ccp4. There are 3 arguments for this program:

Convert orientation matrix to pdb

If an orientation matrix is available (an rmatfile), the (reciprocal) cell parameters can be converted by rmat2pdb to a pdbfile. This pdbfile can be read by coot to display the (reciprocal) lattice on top of the density map.
The minimum set of commands for rmat2pdb are: The lambda, scale and thmax commands can be executed using the name.rmc file created earlier by img2r with the @ operator.
At this stage, you may want to edit the coot script name.coot, created earlier by img2r, change (load "rmat1.scm") into (load "pdbfile.scm") and uncomment this line (remove the leading semicolon).

rmat ic.rmat
write ic

And, after editing, the file recip.coot:
(set-colour-map-rotation-for-map 90)
(set-show-origin-marker 0)
(set-active-map-drag-flag 0)
(set-font-size 3)
(set-views-play-speed 60.00)
(scale-zoom 0.5)
(load "ic.scm")
(handle-read-ccp4-map "recip.map" 0)
(set-last-map-contour-level-by-sigma 5)
(copy-molecule 2)
(set-last-map-contour-level-by-sigma 8)
;(load "rmat2.scm")
(set-map-radius 100)
(set-clipping-front -8)
(set-clipping-back -8)

Display the map in coot

coot is a program to display density maps and molecular models. We will use the program to display reciprocal density maps and reciprocal lattice points.
The following files are used:

Start Coot with coot --script=mapname.coot
Standard views along the axes are available via ExtensionsViewsViews Panel
EVPY Suite Overview