- modeller_usage - salilab.org

Regarding difficult modelling in modeller
by Cn rahul 20 May '20

20 May '20

I used the mGenThreader server to get a .align file as output. How to edit/ convert to respective .ali file as required by modeller python script. Do we have to do it manually ? -- Dr. C N RAHUL Ph: 09666011197 Email: cnrahul(a)gmail.com

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Can the Modeller license be available as a site license?
by ZHANG Cheng 20 May '20

20 May '20

Dear Modeller, I was trying to ask our HPC staff to install the Modeller in HPC, so that we can access it using multiple cores. But I was told: The Software Manager has discovered that the licence is per user and not available as a site license. So can I ask, can a site license be available? Thank you! Yours sincerely Cheng

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How to constrain the computational resources used for Modeller?
by ZHANG Cheng 18 May '20

18 May '20

I need to build a model with over 16,000 residues on Win10 which requires high demand for memory (maybe CPU as well). Can I set the maximum memory MODELLER uses, so that my PC will not freeze, and I can terminate the program without forcing the PC to restart? Thank you!

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missing loop
by Qinghua Liao 16 May '20

16 May '20

Hello, In my protein, there is one missing loop, 15 residues. I used the script from the tutorials to add the missing residues while keeping other coordinates: # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('133', '135'), self.residue_range('217', '230')) a = MyModel(env, alnfile = 'alignment.ali', knowns = '1qg8', sequence = '1qg8_fill') a.starting_model= 1 a.ending_model = 1 a.make() # However, the loops added are too extended, even have bad contacts with the other parts of the protein. As the figure in the Dropbox: https://www.dropbox.com/s/3obtrrvc9c9w8df/image.png?dl=0 Could someone guide me how to add the loop more properly? Thanks a lot! All the best, Qinghua

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Use modeller inside class method - called from an ThreadPoolExecutor
by Pedro Guillem 07 May '20

07 May '20

Hi All, I have a class called Mutant(), its constructor generates a random FASTA sequence. A class method *writeToPDB()* uses modeller to push the FASTA into a template PDB. This is already working very well. If I do 1000 mutants this takes an eternity (one after the other)... so I thought of crafting a ThreadPoolExecutor. Modeller runs inside the class method. Concurrent calls should not share memory with other instances of Mutant(). mutants = [] #Holds an Array of mutant objects executor = ThreadPoolExecutor(max_workers=20) #Thread executor for i in range(1000): mutants.append(Mutant()) executor.submit(mutants[i].writeToPDB, templatePDB) This simply tells the executor to queue a new thread with the writeToPDB() method. When I try to do this, it seems that modeller is being executed in the first call and sharing its state with all subsequent calls... so I get like 90 models (not 1000) written in whatever state modeller was when running the other instances. How can I force a class method to use its own modeller instance?. This is the method: env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') aln = alignment(env) mdl = model(env, file=code) aln.append_model(mdl, atom_files=code, align_codes=code) residue = self.fasta[resid-Mutant.compensate] sel.mutate(residue_type=Mutant.res1to3[residue]) #mutate aln.append_model(mdl, align_codes='mut') mdl.clear_topology() mdl.generate_topology(aln['mut']) mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') name = str(self.pdbpath)+str(self.id)+".pdb" mdl.write(file=name)

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Retain residue IDS when mutating and writing PDB
by Pedro Guillem 05 May '20

05 May '20

I'm using Modeller 9.24 to induce a couple of mutations into a PDB. I noticed that when I execute model.mutate() and export the PDB, the residue indexes are completely different from the original file... ebery residue looses its original position in the sequence and gets renumbered to therever it lands. Is there a way I can force modeller to stick to the original numbering? Best Pedro

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Threading sequence onto template with missing residues
by Ahmad Khalifa 04 May '20

04 May '20

Hello, I have a template with lots of missing residues. I want to thread my target sequence onto the aligned parts of the template that are present without moving my target structure in these areas. In my target sequence, I also wish to know how to skip modeling the missing parts altogether, thus making the job a mere threading of aligned unknown regions onto the known ones. Is there a simple way to accomplish my task without doing too much manual alignment and residue listing? Please do post a code snippet if you can. Thanks a lot.

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Ca-Ca restraints
by Mariana GONZALEZ MEDINA 20 Apr '20

20 Apr '20

Hello, I have observed that the more templates I include in the homology modeling the least Ca-Ca distance restraints I obtain. I can't understand this since I would expect to obtain restraints from missing residues, homology, etc from more templates and therefore more restraints imposed into my model. What could an explanation to this? Thank you! Best, Mariana Gonzalez Medina

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reg: template has extra residues
by Anwesha Mohapatra 14 Apr '20

14 Apr '20

Dear Sir , I am trying to build a model where the template is a homo-6-mer. What changes do I make in the MyModel class? # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances# that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') '''s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') s5 = selection(self.chains['E']).only_atom_types('CA') s6 = selection(self.chains['F']).only_atom_types('CA')''' self.restraints.symmetry.append(symmetry(s1, s2,1.0)) def user_after_single_model(self): *Should I add restraint for each chain ??* *KIndly help me* *Thanks and Regards* *Anwesha*

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Modeller 9.24 release
by Modeller Caretaker 09 Apr '20

09 Apr '20

A new version of Modeller, 9.24, 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 9.24 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.24 adds bug fixes, including updated handling of the MEX and ABU residue types, and adds an option to assign IDs to single chain models. See the Modeller manual for a full change log: https://salilab.org/modeller/9.24/manual/node40.html If you encounter bugs in Modeller 9.24, please see https://salilab.org/modeller/9.24/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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