[phenixbb] pointer distances, recording water

[Maia Cherney]

Hi Paul,
the format of the file got screwed. I am resending the file in the 
attachment.

I would like to repeat the description of the problem.

There is a difference in recording of water molecules in coot and in 
phenix. The example is given in the attached pdb file.

I apologize for the wrong subject (pointer distances), as this was my 
previous request to make pointer distances available to atoms of 
symmetry molecules.

Maia


Maia Cherney wrote:
> 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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