Re: [phenixbb] phenix refine

Hi, This was not necessary it just ran fine with the cif file. thanks, shya

Dear Shya,

So did you rename your glycerol? You have to do that. See http://xray.bmc.uu.se/hicup/GOL/ and http://xray.bmc.uu.se/hicup/GLC/

Best regards, Folmer Fredslund

2009/6/11 :

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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

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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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