[Biopython] Problem writing a PDB with multiple models

[João Rodrigues]

Ah! That you can disable with write_end=False to PDBIO save().

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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