[phenixbb] phenix refine

[Folmer Fredslund]

Dear Shya



2009/6/11  <sbiswas2 at ncsu.edu>:
> 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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