Pymol Tip


had a long-standing problem that was nagging me in Pymol – lone pairs, or more specifically how to remove them easily. This usually occurred when visualising data out of a GOLD docking run, where the software has added lone pairs to active site residues and ligands

The “atoms” look like:

62 **** 45.6415 30.9229 12.1185 LP 1 <1> 0.0000

in the output .mol2 files so the **** “atom” names are clearly not going to be helpful in a command line situation. Usually I just tell people to rerun the docking with the GOLD software told to turn the LPs off but people can’t always get on to our licenses fast enough to repeat jobs.

So after an email to the Pymol mailing list, two answers emerged. One which worked:

remove elem LP

and one which didn’t, at least not for me:

remove resn \*\*\*\*

presumably the second one needs additional juju to all the residues in every chain/ligand etc., but the first one works for me so I haven’t bothered to track down the second


About martin

almost on holidays
This entry was posted in Uncategorized and tagged . Bookmark the permalink.

1 Response to Pymol Tip

  1. Boobalan Pachaiyappan says:

    I have the same problem when I run GOLD docking and attempt to make pretty good pictures using Pymol. I did come up an easy solution.

    I open the gold_protein.mol2 in chemdraw 3D (ultra) sofware

    Then, go to Structure >> Lone Pairs >> Remove

    This easily gets rid of the lone pairs in my gold_protein file. Now I can open this file in Pymol, load ligands and can make nice images without loan pairs.


    -Boobalan Pachaiyappan, Ph. D. (Medicinal Chemistry)

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s