Hi Martin,
The following works well for modified amino acids with refmac
and I presume the same will work with coot. Rather than define
custom links for you CYD ligand to the neighboring Val and Leu,
I would edit the CYD ligand definition to make it an L-peptide
(instead of the "non-polymer" default for the _chem_comp.group)
then refmac (and I presume coot) will recognize the default peptide
bond linkage to the neighboring residues. This way it gets the
distances & angles for the standard peptide bond from the from the
mon_lib_list.cif file and you do not have to define all of the
individual restraints.
Regards,
Mitch
-----Original Message-----
From: Mailing list for users of COOT Crystallographic Software [mailto:[log in to unmask]] On Behalf Of Martin Moche
Sent: Friday, September 19, 2008 1:20 PM
To: [log in to unmask]
Subject: [COOT] Real Space Refine Zone of modified aa
Dear Coot Users,
I am refining a structure with a covalently bound ligand to a cysteine
residue and called cysteine+ligand for CYD. Refmac5 generates a new CYD
dictionary and runs OK. Using the same dictionary in coot allows for
"Real Space Refine Zone" command to be executed without crash, however
the main chain C-N bonds are broken for the residues before and after my
modified CYD residue. Part of my CYD dictionary is listed below but is
this links not recognised by COOT?
How can I use "Real Space Refine Zone" in COOT for a covalently modified
amino-acids (here called CYD).
Best regards,
Martin
# --- DESCRIPTION OF LINKS ---
#
data_link_VAL-CYD
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
VAL-CYD 1 C 2 N . 1.260 0.020
#
data_link_CYD-LEU
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
CYD-LEU 1 C 2 N . 1.260 0.020
# ------------------------------------------------------
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