[Biopython] adding multiple models to one PDB

[Hongbo Zhu 朱宏博]

Hi, João,

AFAIK, "fit" means "superimpose", rather than "align" in PyMOL. That is,
the proteins have to be same, like different models in a NMR structure. It
is unclear if Patrick's proteins are so. Since he mentioned "align", I just
presume he has different proteins.
In addition, PyMOL is quite picky if you ask it to (be) fit :-)
http://www.pymolwiki.org/index.php/Rms

Yes it is getting off topic. I guess Patrick needs to provide more info if
he needs more help.
cheers,
hongbo


On Wed, Feb 25, 2015 at 5:03 PM, João Rodrigues <
j.p.g.l.m.rodrigues at gmail.com> wrote:

> Hi Hongbo,
>
> Slightly off-topic but.. In Pymol you can use intra_fit to align models of
> an ensemble and view the multiple states without splitting.
>
> Cheers,
>
> João
>
> A qua, 25/02/2015, 16:48, Hongbo Zhu 朱宏博 <macrozhu at gmail.com> escreveu:
>
> Hi, Patrick,
>>
>> if you just want to visualized the aligned structures, you can load them
>> one by one in PyMOL. Merging them as different models in one PDB is not
>> necessary. Perhaps it is even not optimal: you have to "split" the models
>> in PyMOL if you want to view them all.
>> You can open multiple PDB files in the same directory using PyMOL by
>> typing:
>> pymol *.pdb
>>
>> You can also align structures within PyMOL. Several methods are available:
>> http://www.pymolwiki.org/index.php/Align
>>
>> cheers,
>> hongbo
>>
>> On Tue, Feb 24, 2015 at 11:45 PM, PC <patrick.cossins at inbox.com> wrote:
>>
>>> Hi,
>>>
>>> I have the following PDB's
>>>
>>> A.pdb
>>> B.pdb
>>> C.pdb
>>> D.pdb
>>>
>>> I can align B, C , D with A but I want to write ALL four structures in
>>> one file to open in a views like pymol.
>>>
>>>         io = Bio.PDB.PDBIO()
>>>         io.set_structure(moving_structure)
>>>         io.save("moved.pdb")
>>>
>>> This has one file, on the second iteration I want to append to moved.pdb
>>> the other pdb's.
>>> How can I do that in biopython?
>>>
>>> Thank you,
>>> Patrick
>>>
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>>
>>
>>
>> --
>> Hongbo
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>


-- 
Hongbo
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