[phenixbb] phenix refine

[Pavel Afonine]

I absolutely agree with those suggesting to rename it.
Glycerol is a standard item from the monomer library, therefore if it is 
named correctly in PDB file then there is no need to run elbow and 
create a CIF file - phenix.refine will recognize it just fine. If 
phenix.refine chocks on it then it means there is something wrong with 
the names and it is the best to fix it right from the beginning, rather 
than keep masking it.

Pavel.


On 6/12/09 7:47 AM, Engin Ozkan wrote:
> But you still have to rename your glycerol. Otherwise, we may not be 
> able to interpret your pdb correctly when you finally publish it. 
> Please always check from HICUP or CCP4 monomer library for the naming 
> (and you can get cif files from there, too).
>
> Engin
>
> On 6/12/09 5:55 AM, sbiswas2 at ncsu.edu wrote:
>> 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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>>>>>>
>>>>>>           
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>>>>>         
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>>
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