Hi Peter,
  If the lysine is dimethylated, the monomer code needed is MLY. 
By mass spec we found most sites to be dimethylated. However,
looking at the structures we found a few sites to be protected 
from methylation. These had clear density for the NZ atom, no 
density for methyl groups and a hydrogen bonding network that 
could explain protection from the dimethylaminoborane reagent.
Regards,
Mitch

P.S. Note that some older versions of the monomer library have a 
MLY.cif file that libcheck expands to give a planer arrangement of NZ and CE, 
CH1, CH2 instead of the proper tetrahedral arrangement.  Looking at the CVS log -
http://www.ccp4.ac.uk/ccp4bin/viewcvs/ccp4/lib/data/monomers/m/MLY.cif 
the CCP4 distributed version of MLY was corrected 9/16/2010 for release-6_1_24.
So if you have an older version of the library -- e.g.
the one distributed with CCP4 release 5.0 - 6.1.12, you will want 
to update your MLY.cif restraint file.	Either from the ccp4 CVS, 
and the one Phil Evans distributed list in 2009
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=CCP4BB&P=R59939&1=CCP4BB
or the one from the current library on Garib's site -- see
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=CCP4BB&P=R60231&1=CCP4BB 
or you can use the one I generated 
http://smb.slac.stanford.edu/~mmiller/MLY_mon_lib-mm2.cif 
which was used for refining 3MC3 3LN3 3IUZ 3HSA 3GS9 2QJV 2I6G 2FTZ 2FCL 2F4I and 
2ETV.

While some programs need the link records to display the bonds, refmac doesn't 
need them if you have the monomer defined as an L-peptide in the restraint file.  
The PDB will generate the necessary LINK records on deposition if they are missing.


-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Robbie Joosten
Sent: Thursday, November 04, 2010 6:27 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] How to add methyl group on the NZ atom of lysine

Hi Peter,
 
Iff you are sure you are dealing with methyl-lysine, you can get it into your structure by using "Get monomer" to get the compound MLZ. Position it correctly and then merge it into the structure. 
I prefer using a text editor to do this. Make sure you put the ATOM records at the right position in the file (otherwise real-space refinement won't work). You probably also need to make LINK records, which you can copy from an existing PDB file (1xer has the links you need).
 
Helix-Turn-Helix,
Robbie Joosten

________________________________
> Date: Thu, 4 Nov 2010 09:04:53 -0400
> From: [log in to unmask]
> Subject: Re: [ccp4bb] How to add methyl group on the NZ atom of lysine
> To: [log in to unmask]
>
>
> Dear All and Peter,
>
> In one of my structure, I find similar positive density though my
> protein was not methylated.
>
> Are there are any other reasons for appearance of such positive density
> next to Lysine.
>
> Thanking you
>
> Yogi
>
>
>
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> peter66 wright
> Sent: Thursday, November 04, 2010 7:26 AM
> To: [log in to unmask]
> Subject: [ccp4bb] How to add methyl group on the NZ atom of lysine
>
>
>
> Dear All,
>
> Could anyone please tell me how to add methyl group in COOT on the NZ
> atom of lysine that has been methylated before crystallisation? The
> density map is attached to this mail from which you can clearly see the
> methyl group should be there, but I do not know how to add.
> Many thanks for help.
>
> Peter