[Chimera-users] superimposition of DNA moleucles

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 5 09:56:01 PST 2014

Hi Urszula,
If you enter exactly the command that I showed earlier, it specifies the same numbers of atoms. That command only used some of the residues. Open monomer file, open DNA-1 file and then enter *exactly* this command:

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


On Mar 5, 2014, at 5:08 AM, Urszula Uciechowska wrote:

> Hi Elanie,
> I corrected the command:
> match #0:DNA-TrfA-complex-NEW-1.pdb:3986-5321
> #1:nucA-DNA-mina99-ch2-NEW.pdb:1-1369
> However the number of my atoms is not equal, can I still do it using this
> command?
> /Urszula
>> 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:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecore.html>
>> 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:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
>> Or, to move by hand you can use the checkboxes under the Command Line to
>> control which one is frozen (un-check to freeze).
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
>> 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
>> ----------
>> 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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