[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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