Electron Density Maps
Read and Contour an Electron Density Map for Crambin
The following two files for the 46-residue plant-seed protein crambin,
derived from the x-ray structure (Brookhaven code 1crn), can be found
in Moloc's data directory moloc/dat: crbn.pdb (structure),
crbn.mpf (calculated electron density map). In order to
save disk space the map resolution is rather low.
- Start Moloc by typing 'Moloc -c crbn.pdb'
- Enter the 'map' (handling maps) menu.
- Choose 'g' (get map). Moloc will present a list
of available formats.
- Select 'Xplor map Formatted (.mpf)'. Moloc will
ask for a file name and then present a list of files, that match
the specification.
- Select 'crbn.mpf' Moloc will read the map and
output various map data e.g. average- and rmsd-values of the map.
- Click 'k' (contour map) to to get a list of maps
available in memory (in our case just 'crbn').
- Select the map, decline the question about interactive mode, and
choose a color for the contour. For small maps interactive mode is
offered, which you might want to try out if you have a fast computer.
- Now, a slider appears for adjusting the contour level.
The slider range corresponds to the occurring map values. Average-
and rmsd values are given in the header.
- Operate the slider by pointing into the field with the yellow
triangle, pressing the LEFT-hand mouse button, and moving the
mouse sideways until you have set the desired contour level.
The actual slider value is given in the field at the far right.
- Select a level of about 2.0 (something above avg.+rmsd).
- Accept the actual value with a RIGHT click in the green 'accept'
field.
- Repeat contouring steps to generate contours at additional levels.
- Contour visibility is governed in the display menu
'./m'
This procedure can be lumped into the startup
of Moloc by writing an input list file, e.g.
crbn.ils, consisting of the the lines:
crbn.pdb yellow
crbn.mpf 2.0 blue 2.6 red
The startup command 'Moloc crbn.ils' will result
starting up Moloc, reading the structure from crbn.pdb
together with the map from crbn.mpf, and contouring the map
at levels 2.0 (blue) and 2.6 (red).
Selecting a Map Region for Display
Suppose you would like to display the map region just about the
side chain of the residue TYR29. Since maps cannot be modified
within Moloc the first step is to transfer
the portion of the map contour that contains the region of
interest into a Moloc entry. To achieve this proceed as follows:
- Select 'v' (visibility) to obtain a list
of contours together with an indication of the visibility
mode.
- Change the visibility mode of contour 2.0 to 'p' =
picking by repeated RIGHT clicks into the corresponding
colored square.
- The contour has disappeared now.
- Select 'r' (set user range) and set the
'pick range' to about 1.
- Click 'b' (make bricks visible by picking atoms)
which will be highlighted.
- Now make contour bricks around TYR29 visible by
picking atoms of its side chain (unpick with MIDDLE mouse).
- If all bricks needed for the side chain of TYR29 are lit
(in this case it is just a single brick), select
'n' (transfer contour into entry).
- From the list of contours that pops up select the 2.0 contour.
- You only want bricks marked as visible (yes/no
requester). The alternative, the whole contour, will lead to
a rather large entry which, for large contours, may take much time
to generate.
- The entry is now superimposed onto the contour, thus, make
the contour invisible to see just the entry (called 'ct2_0').
- Exit the map menu.
To cut off the parts of the contour entry which are not
adjacent to the side chain of TYR29, we can now misuse the entry
building facilities. First we want to
specify the vertices adjacent to the side chain.
- Set the contour entry, 'ct2_0', to active, the protein, 'crbn',
to visible ('.../a').
- Click the 'set' (define sets of atoms)
option to enter the 'set' menu.
- Select 's' (substituents) and pick 'CA'- and
'CB' atoms of TYR29 in this order, to add the side chain atoms to
the current set (e.g. u0).
- Click 'd' (distance criteria from current set)
which will produce a new set consisting of all atoms in
active entries that are within a given range of any atom in
the current set.
- Set the range parameter of the slider to about 2.0 to exclude
the more distant contour vertices. Exit the slider.
- Moloc asks whether the environment is OK, and you may rotate
and examine the set. If you are not satisfied click
'n' to get back to the slider.
- To fine tune your selection you may add or remove vertices
to or from the set with the atom pick option 'a'.
- Memorize the name of the environment set (u1) and
exit the 'set' menu.
Now we cut of the vertices which are not
member of the environment set:
- Click the builder option 'dTp' (topology changes)
- From the 'dTp' menu chose 'd' (delete set of atoms)
which will throw you again into the 'set' menu. Upon leaving the
set menu, the atoms (vertices) of the specified current set will
be deleted.
- Select the whole contour entry ('e' and pick).
- Subtract the previously specified environment set ('u1')
by clicking '!' (not into present set) and
choosing the environment set from the list of sets that pops up.
Upon quitting the list, the corresponding vertices are unmarked.
- Exit from the 'set' menu to have the marked vertices and
adjacent edges removed.
Hopefully the map fragment now locks as you expected.