[Chimera-users] superimposition of DNA moleucles

[Elaine Meng]

Hi Urszula,
You would type the "match" command exactly as I did in the earlier message (do not insert the name of the files!).  That command assumes you opened the monomer file first and then the DNA-1 file.
Best,
Elaine

On Mar 5, 2014, at 4:55 AM, Urszula Uciechowska wrote:

> 
> 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?
> 
> /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