[Biopython] Problem writing a PDB with multiple models

[Claudia Millán Nebot]

Perfect! Thanks a lot again!

2015-10-27 17:07 GMT+00:00 João Rodrigues <j.p.g.l.m.rodrigues at gmail.com>:

> Ah! That you can disable with write_end=False to PDBIO save().
>
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> On Tue, Oct 27, 2015 at 4:39 PM, Claudia Millán Nebot <cmncri at ibmb.csic.es
> > wrote:
>
>> Sorry, I meant the END statement :)
>>
>> 2015-10-27 16:37 GMT+00:00 João Rodrigues <j.p.g.l.m.rodrigues at gmail.com>
>> :
>>
>>> Hi Claudia,
>>>
>>> The TER statement *should* show up at the end of each chain, so it’s OK.
>>>
>>> Best,
>>>
>>> João
>>>
>>>
>>>
>>>
>>> On Tue, Oct 27, 2015 at 3:40 PM, Claudia Millán Nebot <
>>> cmncri at ibmb.csic.es> wrote:
>>>
>>>> Dear Hongbo and João,
>>>>
>>>> thank you both! I got my models named right now, but as João points
>>>> out, the TER keeps appearing.
>>>> Anyway, I am happy that it is something that can be helpful for other
>>>> cases because it is a general problem in the writing of
>>>> the file. I will updgrade my Biopython installation as soon as the fix
>>>> is available. Thanks again! :)
>>>>
>>>> Best,
>>>>
>>>> Claudia
>>>>
>>>> 2015-10-27 13:40 GMT+00:00 Hongbo Zhu 朱宏博 <macrozhu at gmail.com>:
>>>>
>>>>> if you look at PDBIO.py :
>>>>>
>>>>> if model_flag:
>>>>>     fp.write("MODEL      %s\n" % model.serial_num)
>>>>> ​
>>>>> so model.serial_num is written, not model.id.
>>>>>
>>>>> Although the BioPython FAQ says:
>>>>>
>>>>> What is a model id?
>>>>>
>>>>> The model id is an integer which denotes the rank of the model in the
>>>>> PDB/mmCIF file. The model is starts at 0. Crystal structures generally have
>>>>> only one model (with id 0), while NMR files usually have several models.
>>>>>
>>>>>
>>>>> So perhaps one of them should be updated?
>>>>>
>>>>> hongbo
>>>>>
>>>>
>>>>
>>>
>>
>
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