Re: [COOT] A problem about peptide link of special residues

[Paul Emsley]

Garib Murshudov wrote:
Have you declared your modified LYS as L-peptide. It should be be done 
in the beginning like:



data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
LYS  LYS 'LYSINE  'L-peptide  22   9 .



Garib,

Many of the modified lysines in the Refmac dictionary are not marked as 
 L-peptides.   Is that something that needs to be fixed in the dictionary?



Paul.

Re: [COOT] A problem about peptide link of special residues

[Garib Murshudov]

Have you declared your modified LYS as L-peptide. It should be be done  
in the beginning like:



data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
LYS  LYS 'LYSINE  'L-peptide  22   9 .

Garib

On 19 Feb 2009, at 01:30, Feng Yu wrote:


Hi, all

   I have a protein which contains a modified Lys. I have imported  
the correct
cif file, so coot can identify and refine this residue well. But the  
problem is that
the peptide bond between this modified Lys and the normal residue is  
broken. I

wonder how to fix this problem?

   Coot version is coot-0.52

   Thank you!

Feng Yu, yuf...@sinap.ac.cn
Feb 19, 2009