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Re: [modeller_usage] Automatically find gaps in the alignment



Sorry, I'm intruding in the conversation.
But modeller can not automatically detect those gaps without the alignment? or can it? (I mean, for example, comparing the SEQRES with the sequence of each CA ATOM)

thank you very much and sorry again

OCS


Oscar Conchillo Solé
Group of Computational Biology and Proteomics
IBB Data Center Manager and Linux Sysadmin
Institut de Biotecnologia I Biomedicina (UAB)
mail: 
telf: 0034 93581 4431; 0034 93586 8939


On 02/04/2015 05:40 PM, Modeller Caretaker wrote:
On 2/4/15 8:35 AM, Edelmiro Moman wrote:
Great!

But can I insert that directly within the selection like this?

class MyModel(automodel):
     def select_atoms(self):
         return selection(self.get_insertions(aln, minlength=1,
maxlength=30, extension=0, include_termini=True))

Yes - although you'll need to read the alignment first. There's a method read_alignment() which returns it. (Note that this is basically what the default loopmodel.select_loop_atoms() method does, except that it includes deletions too.)

    Ben Webb, Modeller Caretaker