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:

thmax f
Sets the maximum resolution of the image data to f (in degrees).
maxdim n
Sets the size of the reciprocal map to n. The reciprocal map will have dimensions -n:n along each of the laboratory axes (x,y,z)
read imagefiles
imagefiles is a list of images. Wildcharacters (* and ?) are allowed.
contour name
This will create:
- name .cnt
  a cnt file. Basically this file consist of nz 2-dimensional arrays of ny*nx pixels.
- name .coot
  A coot script which will load the density maps and sets various parameters. You may want to edit this file later.
- name.rmc. This file describes the corresponding cnt file. It contains
  - thmax
  - lambda, the wavelength used in the datacollection
  - scale, the scale factor to map pixel numbers in the cnt file to reciprocal values.
  This file can be used by rmat2pdb, which converts rmatfiles to pdb files
exit
Done

Example:

img2r
thmax 15
maxdim 100
read *.sfrm
contour recip
exit

This will create:

recip.cnt. The cnt file containing the reciprocal lattice. The contents of this file can be inspected with the contour command of view.
This file will be converted to a CCP4 densitymap in the next step.
recip.rmc. This file will later be used by rmat2pdb, which converts rmatfiles to pdb files

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:

inputfile. The cnt file created earlier by img2r.
yes for a logarithmic scale or no for a linear scale.
outputfile. The CCP4 density map file to be used by coot.

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:

rmat rmatfile
Read rmatfile
lambda f
The wavelength used in the diffraction experiment
thmax f
The resolution cutoff (specified as theta in degrees). This will be used to limit the size of the generated reciprocal lattice points. You may want to use the same value used earlier with img2r.
scale f
The scale factor used by img2r to map pixel numbers in the density map to reciprocal Ångströms.
write pdbfile
This will create:
- pdbfile -axes.pdb
  A pdb file with (quasi) atoms along the main axes a^*, b^* and c^*
- pdbfile -hkl.pdb
  A pdb file with (quasi) atoms on all lattice points
- pdbfile .scm
  A coot script, which will load pdbfile -axes.pdb and pdbfile -hkl.pdb. Standard views (along a^*, b^* and c^*) will be added to the coot viewlist

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).

Example:

rmat2pdb
@recip
rmat ic.rmat
write ic
exit

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:

mapname .coot
Setup coot, read mapname .map and set contour levels.
In this file will be a (commented) line containing (load "rmat1.scm"). You may want to edit this, uncomment the line, and substitute pdbname .scm
mapname .map
The reprocal denstity map
pdbname scm
Coot script to load two pdb files, and setup views along the main reciprocal lattice vectors.
pdbname -axes.pdb
A pdb file with (quasi) atoms along the reciprocal axes.
pdbname -hkl.pdb
A pdb file with (quasi) atoms on all lattice points

Start Coot with coot --script=mapname .coot
Standard views along the axes are available via Extensions→Views→Views Panel

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