[phenixbb] phenix refine

Pavel Afonine PAfonine at lbl.gov
Thu Jun 11 09:06:17 PDT 2009


Hi Shya,

- use phenix.ready_set:

phenix.ready_set model.pdb

The above command will produce a CIF file that you can use when running 
phenix.refine:

phenix.refine model.pdb data.mtz file_name.cif

- it is a good idea to make sure that your PDB file contains element 
type in column 77 (or 78 - I forgot exactly, check it).

Pavel.


On 6/11/09 8:56 AM, sbiswas2 at ncsu.edu wrote:
> 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       "
>     ... (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
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