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 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

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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 describe where the residues can be, e.g. residues allowed above 10 A in the z direction? Is there a way to specify this? I appreciate any help in advance. Thanks, Shyam

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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 a full change log: https://salilab.org/modeller/9.18/manual/node40.html If you encounter bugs in Modeller 9.18, please see https://salilab.org/modeller/9.18/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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