[Chimera-users] superimposition of DNA moleucles

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 3 09:26:52 PST 2014

Hi Urszula,
There are several problems…  Matchmaker is for automatically pairing chains of same chemical type (both protein or both DNA, for example) and similar sequence.

(1) your PDB files are weird: The monomer file has protein + one DNA strand all as chain A and the other DNA strand as chain B.  Normally in a PDB file these would have three different chain IDs. The  DNA-1 PDB file doesn't have any chain IDs for the two DNA strands, whereas normally these would have two different chain IDs.  For Matchmaker, the combination of protein and DNA into the same chain ID is a problem.  However...

(2) your DNA sequences are not that similar.   In that case you wouldn't want to use MatchMaker anyway, but some other method of superimposing the structures.  Other methods include the command "match," where you must specify exactly which residues and atoms you want to match, or freezing one structure and moving the other one by hand.  The different methods are outlined here:

For example, assuming you just want to put the DNA helices on top of each other, this command will roughly superimpose your structures if model #0 is your monomer file and model #1 is the DNA-1 file (show Command Line using the Favorites menu):

match #0:2-20.a at p #1:2-20 at p

Manual page for the match command: 

Or, to move by hand you can use the checkboxes under the Command Line to control which one is frozen (un-check to freeze).

It is possible to use MatchMaker if you change the setting Matrix: to Nucleic, but since it is trying to match only the parts with similar sequences, the DNA helices are offset.  You can try it and see what I mean.  I thought you probably didn't want that, which is why I suggested the other methods first.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 3, 2014, at 6:29 AM, "Urszula Uciechowska" <urszula.uciechowska at biotech.ug.edu.pl> wrote:

> Dear chimera users,
> I need to supeimpose a DNA molecule DNA-1.pdb into the protein-DNA complex.
> I was trying to do this using Mach Maker, but I am getting errors.
> I am not sure if I can do it using this tool and how should I do it.
> Thank you in advance for any help and suggestions...
> best regards
> Urszula

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