[phenixbb] pointer distances

Maia Cherney chern at ualberta.ca
Fri Mar 26 07:17:42 PDT 2010


Thank you, Paul.

There is also difference in recording water. Should it be ATOM or 
HETATM? Phenix makes it HETATM, but coot makes it ATOM.

Here is an example that was saved after adding one water molecule in 
coot (after refinement in phenix).

HETATM10472  O   HOH S1252      75.727   6.379  70.023  1.00 
31.17           O 
HETATM10473  O   HOH S1253      40.692  -0.062  54.840  1.00 
37.64           O 
TER        10474       HOH 
S1253                                                     
ATOM     10475  O   HOH S1254      75.842   2.043  56.024  1.00 
35.64           O 
TER        10476       HOH 
S1254                                                     
END

Maia


Paul Emsley wrote:
> Maia Cherney wrote:
>> Hi Paul,
>>
>> Coot saves pdb files with TER card. The problem is the TER card takes 
>> the next atom number.
>>
>>
>> ATOM   2303  C4  ADP A 288      33.070   4.240  14.161  1.00 
>> 11.08           C TER      2304         ADP A 288 ATOM   2305  O    
>> SER B  -1
>>
>> The same model after phenix gives no number to the TER card.
>>
>> ATOM   2303  C4  ADP A 288      33.070   4.240  14.161  1.00 
>> 11.08           C
>> TER
>> ATOM   2304  O   SER B  -1
>>
>>
>> As a result, the number of atoms in the pdb files is different. That 
>> is confusing. Could you please fix this problem.
>>
>> Maia
>>
>>   
>
>
> Hi Maia,
>
> It seems to us that this is an issue with Phenix, not Coot or mmdb.
>
> Have a look here:
>
> http://www.wwpdb.org/documentation/format32/sect9.html#TER
>
> "The serial number of the TER record is one number greater  than the 
> serial number of the ATOM/HETATM preceding the TER"
>
> Regards,
> Paul.
>
>
>
>
>



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