Re: [phenixbb] phenix refine

Hi Folmer and Pavel, Thanks for your suggestions. Phenix readyset gave me only .eff and .pdb file so I ran elbow which gave me the cif file as the output and this runs and refines fine now (just to let everyone know). Folmer, the molecule was glycerol and not glucose anyway the problem was the cif file which I could easily generate in elbow. Thanks Shya

Dear Shya

2009/6/11 :

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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 ?

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   ... (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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