Download L01: Desktop Molecular Graphics PyMol 1

Biochem 660 - 2008
Regardless of the number of buttons on your mouse, simply look at the bottom right to
see the corresponding mouse + keyboard action for the following 2 items: MovZ and
Clip.
MovZ will move the object closer or further from your point of view.
Clip will reduce the size of the box into which the object is represented and increase the
contrast with depth-cueing, making parts of the molecule that are further back much
darker.
Playing with these 2 items, it is possible to increase the feeling of depth and 3D feeling
of any represented object and particularly surfaces with deep pockets.
You need to make sure however that the the “depth-cue” option is engaged within the
menu “Display.”
6.2
Measuring distances with the Measurement Wizard.
Distances are measured between two atoms and are expressed in the same unit
as the XYZ coordinates within the PDB file: Angstroms (1Å = 10–10 m).
As an example we shall measure the distance between two atoms within the
carotenoid ligand.
Within the top menu select
Wizard > Measurement
(Note: in older PyMol versions Measurement was called Distance.)
This will create a prompt within the Viewer:
“ Please click on the first atom…”
Within the “Internal GUI” a “Measurement” table
also appears. It can also be used to remove
measurement objects after they are no longer
needed.
Click on the first atom on the ligand
Click on the second atom on the ligand
(you can select the same atoms as in the
examples within the image at right, or select your
choice of atoms)
The default color of the measurement object is
yellow. This can be easily changed with the
familiar ASHLC menu for each measurement, as a
new name is entered within the “Names Panel” for
each distance, e.g. “measure01.”
Change the color to white with the following menu
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