[phenixbb] pointer distances, recording water
Maia Cherney
chern at ualberta.ca
Fri Mar 26 07:33:17 PDT 2010
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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