February 2017 - modeller_usage

model.loops crosses chains
by Shyam Saladi 23 Feb '17

23 Feb '17

Hello -- In the process of using model.loops to identify regions that I will need to model in a multi-chain situation, I have noticed that it returns insertions between chains as a single loop. Furthermore, when specifying insertion_ext > 0, if the loop is at the N- or C-terminus of a chain in the middle of the molecule, the extension crosses to the next chain. Are these two intended behaviors? For the first case, this complicates things for me since I would like to apply restraints to … [View More]each loop separately (which means I need to split up a couple of the loops returned). For the second case, I feel like this may not be the intended behavior since the C terminus of one chain and the N terminus of the next can be far apart in space. Thanks, Shyam ## Reproducible for the first case (can be modified to show the second) ## wget https://files.rcsb.org/download/5KXI.pdb ## remove residues A 74 and B 1 # contents of alignment file: 5xki_fill.aln >P1;2abx structureX:2abx: 1 :A:+148 :B:MOL_ID 1; MOLECULE ALPHA-BUNGAROTOXIN; CHAIN A, B; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC BUNGARUS MULTICINCTUS; ORGANISM_COMMON MANY-BANDED KRAIT; ORGANISM_TAXID 8616; TISSUE VENOM: 2.50: 0.24 IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQP-/ -VCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG* >P1;2abx_fill sequence::::::::: IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG/ IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG* # modeller code from modeller import environ, selection from modeller.automodel import automodel class MyModel(automodel): # only refine loop regions def select_atoms(self): aln = self.read_alignment() loops = self.loops(aln, minlength=1, maxlength=100, insertion_ext=0, deletion_ext=0) for i in loops[0]: print(i) raise ValueError("stop here") return selection(loops).only_std_residues() env = environ() env.io.atom_files_directory = ['.'] a = MyModel(env, alnfile = '2abx_fill.aln', # alignment filename knowns = '2abx', # codes of the templates sequence = '2abx_fill') # code of the target a.starting_model = 5 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling [View Less]

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Excluded volume/Planar spatial restraint
by Shyam Saladi 22 Feb '17

22 Feb '17

Hello, I am trying to model missing residues from a solved structure of a membrane protein to prepare it for MD simulations. Some of these residues (~10) are follow a transmembrane segment at the C-terminus of the protein. After loop refinement, these residues always end up in the "membrane region" that I know from the solved TMs in the structure. However, I know these loop residues are soluble and should not be in this region. I would like to specify some sort of planar spatial restraint to … [View More]

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Modeller 9.18 release
by Modeller Caretaker 22 Feb '17

22 Feb '17

The new version of Modeller, 9.18, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.18 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.18 is primarily a bugfix release relative to the last public release (9.17), although it also adds support for Python 3.6. See the Modeller manual for … [View More]

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