[phenixbb] phenix refine
sbiswas2 at ncsu.edu
sbiswas2 at ncsu.edu
Fri Jun 12 05:55:32 PDT 2009
Hi,
This was not necessary it just ran fine with the cif file.
thanks,
shya
> 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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