Indeed.

The only thing I have to add to this is that after you have your 
modified nucleotide, you might like to try the function

(mutate-by-overlap imol chain-id residue-no tlc)

where imol chain-id and residue-no identify the residue that you
       want to modify (an adenine, I presume (not 6MP))
       tcl is the three-letter-code that you gave to your modified
       residue

Note: mutate-by-overlap is designed to work directly with the output of
libcheck/refmac, I have not tried it with what sketcher provides :)

Paul.


Francis E Reyes wrote:
> There are several ways to do this. One way is the monomer library 
> sketcher route in CCP4. In CCP4, under the refinement tab load the 
> monomer library sketcher. File -> Read File -> Load monomer from 
> library. Then search for the ligand or a related ligand using the pop up 
> box. If your modified base is part of the chain, make sure to choose 
> from the DNA list.  The Geometry and coordinates file will be saved when 
> you choose your ligand. Then use the monomer library sketcher to make 
> substitutions. 
> See http://smb.slac.stanford.edu/public/facilities/software/ccp4/examples/tutorial/html/refine-tutorial.html.
> 
> Save the PDB using Create Library Description. You may want to choose 
> regularize with refmac depending on how the geometries look. In the end, 
> I believe it will use idealized geometries for the entire molecule.
> 
> Then you can import the mon_lib cif file into coot for regularize and 
> real space refine.
> 
> Now as for refinement, you'll need to supply the cif file in one form or 
> another, but you haven't told us what your refinement program is.
> 
> FR
> On Feb 27, 2008, at 1:07 PM, Yu Seon Chung wrote:
> 
>> Hi,
>>
>> I am currently working on refining a protein/DNA complex. I am using 
>> coot to build my model and
>> am wondering if anyone has any experience in dealing with DNA's with 
>> modifications on them? I am
>> working with a N6-methyl-adenine and am having problems with it in 
>> coot. In the library, there is a
>> 6MP (6-methylpurine). Could I use that instead and how do I add 
>> restraints so I can regularize or real  
>> space refine?
>>
>> Thank you,
>> Yu Seon Chung
> 
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
> 
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
> 
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>