[phenixbb] phenix refine

Folmer Fredslund folmerf at gmail.com
Thu Jun 11 23:42:47 PDT 2009


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  <sbiswas2 at ncsu.edu>:
> 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  <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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