[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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