[Biopython] Creating and adding new models to a structure

[life happy]

Hi Iddo Friedberg,

Thanks for correcting me. Its working!!

I have a new question. I like to store an atom list as a model in a
structure.How can I do this?

Kumar.

On Thu, Jul 23, 2009 at 11:09 AM, Iddo Friedberg <idoerg at gmail.com> wrote:

> Kumar:
>
> The following works. The main error you had was that you instantiated
> Select upon definition like so:
> Select = Bio.PDB.Select()
>
> Instead of:
>
> Select = Bio.PDB.Select
>
> Also, you used residue.get_name() instead of residue.get_resname() (there
> is no get_name() method).
>
> #!/usr/bin/python
> import Bio
> import os
> from Bio import PDB
> from Bio.PDB import PDBIO
> from Bio.PDB.PDBParser import PDBParser
> parser = PDBParser()
> mypdb="/home/idoerg/results/libbuilder/einat_blocks/pdb/1ZUG.pdb"
> filehandle = open(os.path.join(mypdb), 'rb')
> structure = parser.get_structure( "1ZUG", filehandle)
> filehandle.close()
> Select = Bio.PDB.Select
> class GlySelect(Select):
>    def accept_residue(self, residue):
> #       print dir(residue)
>        if residue.get_resname()=='GLY':
>            return 1
>        else:
>            return 0
> if __name__ == '__main__':
>     io=PDBIO()
>     io.set_structure(structure)
>     io.save('gly_only.pdb', GlySelect())
>
>
>
> On Thu, Jul 23, 2009 at 10:45 AM, life happy <iitlife2008 at gmail.com>wrote:
>
>> Hi Peter ,
>>
>> Thanks, the links were helpful. But I am facing this problem.
>>
>> from Bio.PDB.PDBParser import PDBParser
>> parser = PDBParser()
>> filehandle = gzip.open(os.path.join("3dh4.pdb"), 'rb')
>> structure = parser.get_structure( "3DH4", filehandle)
>> filehandle.close()
>> Select = Bio.PDB.Select()
>> class GlySelect(Select):
>>    def accept_residue(self, residue):
>>        if residue.get_name()=='GLY':
>>            return 1
>>        else:
>>            return 0
>> io=PDBIO()
>> io.set_structure(structure)
>> io.save('gly_only.pdb', GlySelect())
>>
>> I use this code but I am getting the following error!
>>
>> File "aligned_matches_written_to_new_pdb_file.py", line 34, in <module>
>>    class GlySelect(Select):
>> TypeError: Error when calling the metaclass bases
>>    this constructor takes no arguments
>>
>> I have also tried the example in
>> http://biopython.org/wiki/Remove_PDB_disordered_atoms.I get the same
>> error
>> message. What  does this mean? Any remedy?
>>
>> Secondly, I didn't understand your answer to my question.."In which step
>> are
>> we sending the transformed co-ordinates into the PDB file? " The
>> Superimposer is a black box for me. I give it atom lists, it gives me
>> RMSD.
>> But I want the aligned co-ordinates of the given atom lists, so that I can
>> see the alignment in PyMol.I don't know how to extract aligned atom
>> co-ordinates!
>>
>> Your example :-
>>
>>
>> http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/protein_superposition/?fromGo=http%3A%2F%2Fgo.warwick.ac.uk%2Fpeter_cock%2Fpython%2Fprotein_superposition%2F
>>
>> does this job perfectly.It aptly prints out aligned models into a new PDB
>> file.But I am working on two atom lists from two different proteins,
>> unlike
>> two models of same structure.Can you give me little push on how to deal
>> superimposing two different structures?
>>
>> sincerely,
>> Kumar.
>>
>>
>> On Tue, Jul 21, 2009 at 1:48 PM, Peter <biopython at maubp.freeserve.co.uk
>> >wrote:
>>
>> > On Tue, Jul 21, 2009 at 9:35 PM, life happy<iitlife2008 at gmail.com>
>> wrote:
>> > > I have tried using   io.save("pdb_out_filename",
>> > se.accept_model(alt_model))
>> > >
>> > >        I get error as , 'int' object has no attribute 'accept_model'
>> >
>> > If "se" really is an integer, that isn't surprising!
>> >
>> > > If I use  io.save("pdb_out_filename", se = accept_model(alt_model))
>> > >
>> > >       I get Error: name 'accept_model' is not defined
>> > >
>> > > In both the cases I created 'se' an object of Bio.PDB.Select()
>> > > Do you have an example for printing out some part of PDB?
>> >
>> > The examples here may help:
>> > http://lists.open-bio.org/pipermail/biopython/2009-May/005173.html
>> > http://biopython.org/wiki/Remove_PDB_disordered_atoms
>> > http://lists.open-bio.org/pipermail/biopython/2009-March/005005.html
>> >
>> > See also pages 5 and 6 of the Bio.PDB documentation, the bit
>> > on the Select class:
>> > http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf
>> >
>> > Peter
>> >
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
>
> --
> Iddo Friedberg, Ph.D.
> Atkinson Hall, mail code 0446
> University of California, San Diego
> 9500 Gilman Drive
> La Jolla, CA 92093-0446, USA
> T: +1 (858) 534-0570
> http://iddo-friedberg.org
>
>