[ccp4bb] modified amino acid connection to protein

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CCP4bb <-- 2008 <-- February 2008 <-- 26 February 2008

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Subject: Re: unknown symmetric density
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2008-02-26

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Subject: 2008 Hybrid Methods Meeting
From: Wes Sundquist wes {- at -} BIOCHEM {- dot -} UTAH {- dot -} EDU
Date: 2008-02-26

Subject: modified amino acid connection to protein
From: Catherine Regni regnicat {- at -} YAHOO {- dot -} COM
Date: 2008-02-26

Hi everyone,

I'm trying to refine a structure with a modified amino acid. I'm running into problems connecting my modified amino acid to the protein (making a C-N bond). Refmac runs fine, but gives an error, "link found between C - N1, not to be used." Here is what I'm doing-- any insights to what I'm missing would be greatly appreciated.

I've added a LINK record to my pdb file, and below is the LINK record from my dictionary generated via ccp4i gui review restraints-- the modified residue is XXX:

# --- LIST OF LINKS ---
#
data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
ALA-SUU ALA . . SUU . .
bond_ALA-C_=_XXX-N1

# --- DESCRIPTION OF LINKS ---
#
data_link_ALA-SUU
#
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
ALA-XXX 1 C 2 N1 . 1.260 0.020
# ------------------------------------------------------

Catherine Regni, Ph.D.

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CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 26 February 2008

Previous message:
Subject: Re: unknown symmetric density
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2008-02-26

Next message:
Subject: 2008 Hybrid Methods Meeting
From: Wes Sundquist wes {- at -} BIOCHEM {- dot -} UTAH {- dot -} EDU
Date: 2008-02-26