My software notes

October 6, 2011

[PyMOL] assign secondary structural regions

Filed under: Uncategorized — kpwu @ 3:25 pm
Tags: , , ,


Sometimes I displayed the cartoon view of a protein in PyMOL as the figures shown below that I don’t really see the helix and strands.

It often happens when I merged 10 or 20 structures into a NMR ensemble file. All 20 structures are aligned but the secondary structural regions are not clearly displayed in PyMOL (commands: set all_states, on)

PyMOL provides two simple means to quickly draw helices and strands on the target proteins.

1. use command “dss”.

Simply type “dss” in the command line, PyMOL automatically calculates, rebuilds and draw the secondary structural regions. If the “all_states” is turned on, all structures will also be displayed properly. Here are two figures show the results of “dss” with single and all 20 states of my target protein.

The command “dss” provides simple but quick way to draw helical and strand regions, however, using other programs such as “DSSP” or “STRIDE” to clearly define the regions of helices and regions is highly recommended.

2. Use command “alter”

As I just said, “dss” doesn’t work perfectly. In this example case, I found length of first two sheets are not long enough, and the loop is a bit longer. I can use command “alter” to manually assign the secondary structural regions of my target proteins.

alter 3-9/, ss=’H’
alter 12-18/, ss=’H’

The above 3 lines are the commands I typed in and the sheets are now longer (see the right up corner). To change the length of loop and sheets, just type alter xx-yy/, ss=’L’, and alter aa-bb/, ss=’S’, respectively.



Create a free website or blog at