[Biopython] Best way to change the chain identifiers of a set of residues

[João Rodrigues]

Hi Claudia, you can use the build_peptides() function from the
Bio.PDB.Polypeptides module. This should give you directly the fragments of
the structure, based on a distance criterion. For the chain, you have to
create new chains.

I'm on my phone so I can't verify it, but I'd first create a new empty
structure (and model), get the fragments of the parsed structure, and then
based on the fragment length add then to the new structure with a
sequential chain ID. I think this is the optimal way.

What Jordan suggested works wonders if you want to filter a given
structure. If you want just to remove small fragments, you could just tag
these residues with a negative bfactor for example and then use this to
filter with Select() and PDBIO().

Cheers,

João

A qui, 26/11/2015, 14:44, Claudia Millán Nebot <cmncri at ibmb.csic.es>
escreveu:

> Hi Jordan, the removal of the residues is working, is the renaming of the
> chains that is causing trouble. I attach an example of input/output
> produced by the function.
>
>
> 2015-11-26 9:09 GMT+00:00 Jordan Willis <jwillis0720 at gmail.com>:
>
>> Also, the detach_child method should work in place, so I’m not sure why
>> this is not working. Can you give an example PDB?
>>
>> Jordan
>>
>> On Nov 25, 2015, at 12:16 PM, Claudia Millán Nebot <cmncri at ibmb.csic.es>
>> wrote:
>>
>> Dear all,
>>
>> I am writing a function that examines a structure, and if there are
>> discontinuous regions that are smaller than a certain size, they will be
>> removed from the structure. Then, I would like to write the structure as a
>> pdb in which the chain identifiers are different for each discontinuous
>> fragment. For that purpose, I want to change the chain id of certain
>> residues. ¿What will be the best way to do it? Because right now it is not
>> working, of course, because I am iterating over something that I am trying
>> to change at the same time. Maybe I am missing something very obvious or
>> straightforward, but I do not see what will be the best way to do it...
>> ¿Maybe creating and empty chain and using the set_parent method?
>>
>> The current code looks like this:
>> def trimByContinuityLimit(pdb_file,min_size):
>>     parser=PDBParser()
>>     structure=parser.get_structure(pdb_file[:-4],pdb_file)
>>     residues=Selection.unfold_entities(structure,'R')
>>
>> list_id="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz1234567890"
>>     dictio_chainid={}
>>     residues_to_remove=[]
>>     current_listres=[]
>>     index=0
>>     for i in range(len(residues)-1):
>>         res1=residues[i]
>>         res2=residues[i+1]
>>         id1=res1.id
>>         id2=res2.id
>>         check=Bioinformatics.checkContinuity(res1,res2)
>>         #print 'check',check
>>         #print 'list_id[index]',list_id[index]
>>         if check==True:
>>             #print "These two residues are consecutive",res1,res2
>>             if id1 not in current_listres:
>>                 current_listres.append(id1)
>>             dictio_chainid[id1]=list_id[index]
>>             if id2 not in current_listres:
>>                 current_listres.append(id2)
>>             dictio_chainid[id2]=list_id[index]
>>             #print 'list_id[index]',list_id[index]
>>             #print 'id1,dictio_chainid[id1]',dictio_chainid[id1],id1
>>             #print 'id2,dictio_chainid[id2]',dictio_chainid[id2],id2
>>         elif check==False:
>>             #print "These two residues are not consecutive",res1,res2
>>             if id1 not in current_listres:
>>                current_listres.append(id1)
>>                dictio_chainid[id1]=list_id[index]
>>             if len(current_listres)<min_size:
>>                residues_to_remove.extend(current_listres)
>>             if i==len(residues)-2 and min_size>1: # If we reach this
>> point, then the last residue is not continuous so it is single :
>>                residues_to_remove.append(id2)
>>             else:
>>                current_listres=[]
>>                current_listres.append(id2)
>>                index=index+1
>>                dictio_chainid[id2]=list_id[index]
>>     # Remove the residues and write the pdb
>>     for model in structure:
>>        for chain in model:
>>            for residue in chain:
>>                id_res=residue.id
>>                if id_res in residues_to_remove:
>>                    chain.detach_child(id_res)
>>                else:
>>                    chain.id=dictio_chainid[id_res]
>>     io=PDBIO()
>>     io.set_structure(structure)
>>     io.save(pdb_file[:-4]+'_trimmed.pdb',write_end=False)
>>
>> Thanks in advance :)
>>
>> Claudia
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