[Chimera-users] superimposition of DNA moleucles

Urszula Uciechowska urszula.uciechowska at biotech.ug.edu.pl
Wed Mar 5 04:55:45 PST 2014

Hi Elaine,

Thank you very much for your help. I was able to superimpose it using your
advices. I want to also try it  by using command "match" as you also
recommended ( please see below).

match #DNA-TrfA-complex-NEW-1.pdb:3986-5321 at p
#nucA-DNA-mina99-ch2-NEW.pdb:1-46 at p

However I am getting error: "Error in DNA-TrfA-complex-NEW-1.pdb:3986-5321 at p
value must be intiger"

How could I correct the command?


> 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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