[Biopython] Problem writing a PDB with multiple models

[João Rodrigues]

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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