Re: [ccp4bb] modified amino acid
Check the cid file has labelled this modified amino acid as L-peptide.. it is in the records at the top. REFMAC tries to link anything labelled as peptide which is a) close to its links and b) numbered appropriately only if that L-peptide flag is there.. Eleanor On 30 May 2015 at 16:40, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Hello, did you check what the log file of refmac says? It may give a clue about what is going on. Regards, Tim On 05/29/2015 11:26 PM, Bio Physics wrote: Hi all, I have a modified amino acid (covalent complex), during refmac5 refinement it isolated from next residues. Phenix does well though with the same .cif file. I know people are doing this every day in refmac. Any help please? -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
Re: [ccp4bb] modified amino acid
Hello, did you check what the log file of refmac says? It may give a clue about what is going on. Regards, Tim On 05/29/2015 11:26 PM, Bio Physics wrote: Hi all, I have a modified amino acid (covalent complex), during refmac5 refinement it isolated from next residues. Phenix does well though with the same .cif file. I know people are doing this every day in refmac. Any help please? -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
[ccp4bb] modified amino acid
Hi all, I have a modified amino acid (covalent complex), during refmac5 refinement it isolated from next residues. Phenix does well though with the same .cif file. I know people are doing this every day in refmac. Any help please?
Re: [ccp4bb] modified amino acid
On 17/05/11 15:35, Afshan Begum wrote: Dear All, I would like to introduce carbamylated lysine in a structure because i have used beta-mercaptoethanol in a protein solution and lysine was carbamylated with this but i faced a problem to introduce this residue in my structures i have not find modified residues in a list of COOT program. So, what are simple approaches to do so. . 5.17.3 http://www.biop.ox.ac.uk/coot/doc/coot/Mutation.html
[ccp4bb] modified amino acid connection to protein
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. 1.2600.020 # -- Catherine Regni, Ph.D. - Looking for last minute shopping deals? Find them fast with Yahoo! Search.
[ccp4bb] modified amino acid connection to protein again
Hi everyone, (sorry for posting twice, I found typos in the original post) 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-XXX ALA ..XXX . . bond_ALA-C_=_XXX-N1 # --- DESCRIPTION OF LINKS --- # data_link_ALA-XXX # 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. 1.2600.020 # -- Catherine Regni, Ph.D. - Looking for last minute shopping deals? Find them fast with Yahoo! Search.
Re: [ccp4bb] modified amino acid connection to protein
Dear Catherine Is your SUU an amino acid modified on the side chain side? If yes then you can use standard peptide links. For this your SUU should be declared as L-peptide in the description. Can you send description of your SUU and I can try to sort out what is going on. Garib On 26 Feb 2008, at 22:47, Catherine Regni wrote: 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. 1.2600.020 # -- Catherine Regni, Ph.D. Looking for last minute shopping deals? Find them fast with Yahoo! Search.
