There isn't an easy way to do this, as far as I know. `pair_fit` can be used to do a superposition based on an arbitrary alignment, but it is very tedious to specify each aligned pair individually, and it's hard to modify the alignment.

I've used NCBI's Cn3D program for detailed manual alignments, as it has a good alignment editor and can show the superpositions internally after each modification. However, it doesn't output two-model pdb files like most of the structure alignment tools (eg's structure comparison tool). Thus you still might have to write an arduous pair_fit command (or a python script to parse cn3 file) if you want to get it into pymol for nice graphics. Cn3D has a confusing interface, so if you want to try it out I can send you my notes on creating alignments off-list.


On Mon, Apr 7, 2014 at 9:11 PM, Lapolla, Suzanne M (HSC) <> wrote:
This worked--thanks. I have another ? that may have been addressed previously but do not know the answer.  Is there a way to do an alignment (or maybe docking is a better word) on two structures/selections and input a constraint for that alignment? For example, i am working on generating a model RE a dimer of two molecules, and I have some data suggesting a range of distances between certain residues of the selection. Is there a way to input that data into Pymol before it completes the alignment, or do I need to use other docking programs to do that? Hope that makes sense.  Thanks.
From: Lapolla, Suzanne M (HSC)
Sent: Friday, April 04, 2014 5:11 PM
To: Thomas Holder
Subject: RE: [PyMOL] manual superposition with pymol

Thank you! I will try this and get back to you.
From: Thomas Holder []
Sent: Friday, April 04, 2014 3:16 PM
To: Lapolla, Suzanne M (HSC)
Subject: Re: [PyMOL] manual superposition with pymol

Hi Suzanne,

looks like you only deprotected the CA atoms. If you have this as a named selection, try "A > modify > complete > molecules" and deprotect again. Or type:

PyMOL> deprotect bymol (sele)

Instead of working with one object and protecting/deprotecting of subsets of atoms, I suggest to extract the selection that you want to move to its own object. That's usually easier to handle.


On 04 Apr 2014, at 13:38, Lapolla, Suzanne M (HSC) <> wrote:

> I am using pymol 1.3 and having trouble with doing manual superposition with my structures. I am able to download my structures, select the portion I want to move manually and, after deprotecting it using the action menu move it using the shift-mouse editing command. When I do this with my selection shown in cartoon mode, things look great, but then when i switch to show my selected residues as  sticks,  the sticks become huge --they  get bigger  and/or  smaller as I move the structure.  Ideas on what I may be doing wrong? Hope this makes sense. Thanks, Suzanne

Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Put Bad Developers to Shame
Dominate Development with Jenkins Continuous Integration
Continuously Automate Build, Test & Deployment
Start a new project now. Try Jenkins in the cloud.
PyMOL-users mailing list (
Info Page: