[Chimera-users] Modeller missing residues

[Elaine Meng]

Hi Danilo,
We aren’t the Modeller group… this is the UCSF Chimera mailing list, and I don’t know the answer to your question.  Instead, you may want to look at the Modeller FAQ or wiki, or ask a question on the Modeller forum:

<https://salilab.org/modeller/discussion_forum.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 19, 2019, at 3:34 AM, Danilo Boškovic <a01406823 at unet.univie.ac.at> wrote:
> 
> Dear all,
> 
> I have just made a model according to the tutorial for missing residues for Modeller. I wanted all atoms not to move so i used the script at the bottom of the tutorial. It seems to work but when i do match align i can still see a very very slight misalignment in certain areas that are not supposed to be touched. I used residue ranges from the alignment window by just clicking on residues and reading their positions at the bottom of the alignment window (might be an issue with numbering?). As a starting structure i used the structure i wanted to take the loops from and as a template structure i used the structure in which i wanted to fill the loops (100% same, difference is in states). I edited the script in chimera as follows:
> 
> from modeller import *
> from modeller.automodel import *
> 
> namelist = open( 'namelist.dat', 'r' ).read().split('\n')
> tarSeq = namelist[0]
> template = tuple( [ x.strip() for x in namelist[1:] if x != '' ] )
> 
> log.verbose()
> 
> env = environ()
> 
> env.io.atom_files_directory = ['.', './template_struc']
> 
> class MyModel(automodel):
> 		def select_atoms(self):
>                    return selection(self.residue_range('312', '315'),
>                    self.residue_range('630', '642'),
>                    self.residue_range('668', '674'))
> 		#code overrides the special_restraints method
> 
> 		#def special_restraints(self, aln):
> 
> 		#code overrides the special_patches method.
> 		# e.g. to include the addtional disulfides.
> 		#def special_patches(self, aln):
> 
> a = MyModel(env, sequence = tarSeq,
> 		# alignment file with template codes and target sequence
> 		alnfile = 'alignment.ali',
> 		# PDB codes of the templates
> 		knowns = template)
> 
> a.starting_model = 1
> a.ending_model = 1
> loopRefinement = False
> 
> a.assess_methods = (assess.GA341, assess.normalized_dope)
> 
> a.make()
> 
> Link to tutorial:
> https://salilab.org/modeller/wiki/Missing%20residues