[phenixbb] phenix refine

[sbiswas2 at ncsu.edu]

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
>>>
>>>
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>