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Dear Shya
2009/6/11
Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J "
First of all, glycerol should be called GOL not GLC. Do you mean glucose ?
... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69
Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42
Does anyone know how to resolve this thanks, Shya
You need a cif file for the extra molecule. Can be found at eg. the HICup server (http://xray.bmc.uu.se/hicup/) Best regards, Folmer Fredslund
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