Mode Group

This group contains various modes a user can enter for visualization and editing. 

The Sculpting button lets the user enter sculpting mode in which all aspects of the molecule or protein can be manipulated.  The balloon pop up over the button details the controls, which are: Ctrl + Right click to drag a single atom, and Ctrl + Left click to rotate bonds.  This can be useful for a variety of tasks, but cannot be depended on for accurate representations of molecules in three dimensional space.

The Measurement Tool button lets a user determine the distance between two atoms in a given molecule or protein.  Once a user enters measurement mode they must click on the first atom, and then the second atom to get a distance.  This will be shown by a dashed yellow line with a number midway through it.  To turn off measurement mode the user must use the internal GUI on PyMOL, in which other options are also provided.

The Sequence Viewer button can be used to view the sequence of a protein, peptide, DNA, RNA, and numerous other components of molecules.  There are four different modes for the sequence viewer.  There is a One letter mode which displays the sequence of a protein in one letter format corresponding to the standard one letter code assigned to amino acids.  Three letter mode displays the sequence corresponding to the standard three letter code assigned to amino acids.  AA atoms displays every single atom in the molecule and shows them linearly by residue number, and goes by a nomenclature indicating where in the amino acid the atom resides.  This nomenclature must be looked up for more information.  The last mode is Chains which simply shows all chains in the protein according to the alphabetized name they have been given.  When viewing any of the first three modes it can be difficult to discern where one peptide chain ends and another begins.  This is illustrated in the following picture.

The beginning of a new chain starts with the a space between the two chains, and then a / and the letter of the new chain.  An easy tool to find where chains start and end is to use the "Color by Chain" preset, which will result in the sequence viewer coloring each chains listed residues separately, as shown above.

Advanced Toolbox Tab