Thanks Mitch! Changing "non-polymer" to "L-peptide" in my ligand dictionary was all needed to get "Real Space Refine Zone" in COOT going.
Cheers, Martin __________________________________________________ ----- Original Message ----- From: "Miller, Mitchell D." <[EMAIL PROTECTED]> Date: Friday, September 19, 2008 11:02 pm Subject: RE: [COOT] Real Space Refine Zone of modified aa To: Martin Moche <[EMAIL PROTECTED]>, [email protected] > 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:[EMAIL PROTECTED] On Behalf Of Martin Moche > Sent: Friday, September 19, 2008 1:20 PM > To: [email protected] > 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 > modifiedamino-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 > # ------------------------------------------------------ >
