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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. 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: 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. Now we cut of the vertices which are not member of the environment set: Hopefully the map fragment now locks as you expected.