Electron Density Tools

This group contains numerous options for viewing electron densities of proteins.  The calculations performed are derived from the PDB file parameters, and thusly these options can only be used on PDB files, and not on any constructed peptides or molecules.

The Mesh, Dots, and Surface buttons all superimpose an electron density map calculated by PyMOL in the respective representation over an entire PDB file. 

 The Mesh Select, Dots Select, and Surface Select buttons only work if a user has selected a portion of the protein or molecule in the PDB file.  It is also contingent upon the selection retaining the name "sele" on the PyMOL internal GUI.  If a user changes this name through manual commands on the PyMOL command line, then they will also not work.  Once a user has selected the portion they would like to superimpose the electron density representation over they can press one of these three buttons and it will superimpose the density over only the selected area.  Selecting a new area after this and pressing another selection will make the map over the previous selection disappear, and will superimpose it over the new selection.  Thus if a user wants to superimpose a map over various selections spread out through a protein it is suggested that they use the sequence viewer to selectively choose the amino acids they are interested in.

The Roving Mesh and Roving Surface buttons both superimpose a map limited a small area of the protein.  This map can be moved along the protein to view only a small area at a time on the protein using the middle mouse button.  After clicking either of these buttons a user must hold down the middle mouse button and move the mouse cursor across the protein to drag the map along with it.  To zoom or orient on a specific part of the protein the user can double click the middle mouse button, and the screen will center on this portion and superimpose the map over it.  The breadth of the map that is superimposed can be controlled with the Roving Detail slider .  The larger the number put on the slider, the larger the amount of protein that is superimposed with the map.  After changing the number on the Roving Detail slider, the user must click again on either the Roving Mesh or Roving Surface button to enact the change.

The Double Resolution button is used to increase the definition of the map, resulting in either more mesh lines, and a more distinct and full view of the map, or an increase in the amount of dots, also resulting in a more distinct a full view of the map.  This helps to provide a more accurate and defined view of the map.  Unfortunately doubling the resolution once will take up four times as much memory, and only high end computers can double the resolution more than once.  Therefore it is suggested that a user does not use the Double Resolution button more than once, because it may lead to PyMOL crashing due to a lack of memory resources, and thusly a loss of unsaved work.

The Contour Slider controls the volume taken up by the electron density map that has been created.  Lower numbers make it take up a small volume and lowers the map closer to the protein backbone over which it is imposed.  Higher numbers inflate it significantly and results in a larger volume expanded further away from the protein backbone.  Once a number has been changed on the Contour slider the user must click again on their representation of choice to effect the change.  Use of the Contour slider is suggested only for advanced use and individuals who understand the effect of changing the contour level upon the accuracy of the map.

External Electron Density Mapping

For advanced users

The External Map button brings up a new window with many of the same options as on the normal Electron Density Mapping group.  The difference resides in the fact that this tool is used for importing externally generated electron density maps derived from experimental X-Ray crystallographic data. 

The entry field on the bottom right side of the window, with a label "Input PDB code" above it, is used to bring the user to a database of electron density maps.  Once a user has input a known PDB code into the entry field, they must then press the Get Map button.  This will take them directly to a download page for a map corresponding with the PDB code they have entered. 

Many PDBs are supported by this database, but some are not, so it is not guaranteed that they will have the PDB a user is looking for.  Unfortunately there is no way to prevent the website from loading if it is indeed not supported.  The user will find out immediately after pressing the "Generate Map" button the on the webpage, and it will be returned that the map does not exist. 

There is a dropdown selection menu on the webpage for "Map format", and the user must choose either O (the default), or CCP4, as these are the only two formats supported by PyMOL.  Once the format has been selected click on the "Generate Map" button.  Once the map has been generated it will display a link to the file that has been created.  Right click on this file and select "Save Target As".  This will allow the user to download the file to a specified path.  After this it must be unzipped from its gunzip format.  This will require something like Winzip, or WinRAR, or another unzipping utility that supports gunzip files. 

After this the file can be loaded by PyMOL.  This can be accomplished either through PyMOL itself, or the Load Map button.  Since it is just a map the user will not be able to see anything at first.  To visualize the downloaded map the user must input a name for the map in the Name Object entry, any name will do.  This allows for PyMOL to manipulate the map.  The user must also input the exact name of the file that they just downloaded in the Map Filename entry .  If the user plans on opening a PDB file to superimpose the downloaded map over it is also necessary to name the map something other than the PDB file name.  Example:  Using the PDB 1CHO and having downloaded the map 1CHO it is best to name the map 1CHOmap.  This means in the entry field for filename I would now put 1CHOmap.  This prevents PyMOL from getting confused over inconsistencies with file type and the commands it is being given.  It is also best to input a name for the map in the Name Object entry that is different from the PDB file name.

Once the map has been named and the file name input it is now possible to visualize the map.  The Mesh, Dots, and Surface buttons all do the same thing as previously explained.  The Mesh Select, Dots Select, and Surface Select buttons can only be used if a PDB has also been loaded, and has a portion selected.  The same rules apply to this selection method as mentioned previously.  The Contour scale also operates by the same mechanism as mentioned previously.

There is also a Help button on this interface which provides a quick reference for doing all that has been explained, although it is not as detailed as what has just been laid out. 

Advanced Toolbox Tab