- modeller_usage - salilab.org

Can't really edit my script
by Casey Becker 11 Jun '20

11 Jun '20

Hello, I'm new to modeller and I'm eventually trying to make several hundred models using multiple cpus, however it seems I can't change anything in my script except number of models without causing the system to break and not work. No error pops up, it simply says the task completed instantaneously, doesn't make any models, and doesn't pop up the ok_model window. My script is below from modeller import * from modeller.automodel import * # ---------------------- namelist.dat -------------------------------- # A "namelist.dat" file contains the file names, which was output from # the Modeller dialog in Chimera based on user's selection. # The first line it the name of the target sequence, the remaining # lines are name of the template structures namelist = open( 'namelist.dat', 'r' ).read().split('\n') tarSeq = namelist[0] template = tuple( [ x.strip() for x in namelist[1:] if x != '' ] ) # ---------------------- namelist.dat -------------------------------- # This instructs Modeller to display all log output. log.verbose() # create a new Modeller environment env = environ() # Directory of atom/PDB/structure files. It is a relative path, inside # a temp folder generated by Chimera. User can modify it and add their # absolute path containing the structure files. env.io.atom_files_directory = ['.', './template_struc'] # create a subclass of automodel or loopmodel, MyModel. # user can further modify the MyModel class, to override certain routine. class MyModel(automodel): def customised_function(self): pass #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) # index of the first model a.starting_model = 1 # index of the last model a.ending_model = 5 loopRefinement = False # Assesses the quality of models using # the DOPE (Discrete Optimized Protein Energy) method (Shen & Sali 2006) # and the GA341 method (Melo et al 2002, John & Sali 2003) a.assess_methods = (assess.GA341, assess.normalized_dope) # ------------------------- build all models -------------------------- a.make() I've tried changing the MyModel part to just be automodel, because I was told it was a custom subclass and needed special treatment, which broke the code. I also tried changing the knowns = template to knowns = my template ID. It also broke the code. Thanks.

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Parallel job
by Casey Becker 09 Jun '20

09 Jun '20

Hello, I'm fairly new to modeller, and I'm trying to run a parallel job. I can't seem to get the 'from modeller.parallel import *' line to work. When I input it, no models are created. I have python 3.8 installed, and I'm not sure why it's happening. My script is below. from modeller import * from modeller.automodel import * from modeller.parallel import * j= job() j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) log.verbose() env = environ() env.io.atom_files_directory = ['.', './template_struc'] # create a subclass of automodel or loopmodel, MyModel. # user can further modify the MyModel class, to override certain routine. class MyModel(automodel): def customised_function(self): pass #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) # index of the first model a.starting_model = 1 # index of the last model a.ending_model = 100 loopRefinement = False # Assesses the quality of models using # the DOPE (Discrete Optimized Protein Energy) method (Shen & Sali 2006) # and the GA341 method (Melo et al 2002, John & Sali 2003) a.assess_methods = (assess.GA341, assess.normalized_dope) a.use_parallel_job(j) a.make() I'm still figuring my way out around this. Any help appreciated. Thanks.

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Identical output for different batches
by ZHANG Cheng 08 Jun '20

08 Jun '20

Dear MODELLER, In order to generate hundreds of PDBs, I submit multiple jobs to the cluster. The input template is the same for all the jobs. For each job (i.e. each batch), 10 PDBs are generated. The 10 PDBs within the same batch are different in their "Objective Function" in the PDB remark. But the PDBs between the batches have the same "Objective Function". For example,  ) the 3rd PDB in Batch 1 has the same "Objective Function" as the 3rd PDB in Batch 5 ) the 6th PDB in Batch 2 has the same "Objective Function" as the 6th PDB in Batch 10 So it seems that all the jobs are started from a same "seed". Is there a way to randomise the seed? Thank you! Cheng The script I use is: from modeller import * from modeller.automodel import *    # Load the automodel class log.verbose() class MyModel(automodel):     def special_patches(self, aln):         # Rename both chains and renumber the residues in each         self.rename_segments(segment_ids=['A', 'B', 'C', 'D','E', 'F','G', 'H','I', 'J','K', 'L','N', 'O','M', 'P','Q', 'R','S', 'U','V', '1','2', '3','4', '5','6', '7','8', '9',],                              renumber_residues=[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])         # Another way to label individual chains:         self.chains[0].name = 'A'         self.chains[1].name = 'B'         self.chains[2].name = 'C'         self.chains[3].name = 'D'         self.chains[4].name = 'E'         self.chains[5].name = 'F'         self.chains[6].name = 'G'         self.chains[7].name = 'H'         self.chains[8].name = 'I'         self.chains[9].name = 'J'         self.chains[10].name = 'K'         self.chains[11].name = 'L'         self.chains[12].name = 'N'         self.chains[13].name = 'O'         self.chains[14].name = 'M'         self.chains[15].name = 'P'         self.chains[16].name = 'Q'         self.chains[17].name = 'R'         self.chains[18].name = 'S'         self.chains[19].name = 'U'         self.chains[20].name = 'V'         self.chains[21].name = '1'         self.chains[22].name = '2'         self.chains[23].name = '3'         self.chains[24].name = '4'         self.chains[25].name = '5'         self.chains[26].name = '6'         self.chains[27].name = '7'         self.chains[28].name = '8'         self.chains[29].name = '9' env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env,             alnfile  = '../../1_raw/JN254802-5tx1.ali' ,     # alignment filename             knowns   = '5tx1',              # codes of the templates             sequence = 'JN254802')              # code of the target a.starting_model= 1                # index of the first model a.ending_model  = 10                # index of the last model                                    # (determines how many models to calculate) a.make()                           # do comparative modeling

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Command not found, no module named 'modeller' errors
by Xiao Ran Luo 29 May '20

29 May '20

Hello, I just downloaded version 9.24 of Modeller onto by macOS version 10.14.1 using Homebrew, but when I try to run the first few lines of the basic tutorial, I get a lot of "command not found": Luos-Air:~ luoxiaoran$ >P1;TvLDH -bash: TvLDH: command not found Luos-Air:~ luoxiaoran$ sequence:TvLDH:::::::0.00: 0.00 -bash: sequence:TvLDH:::::::0.00:: command not found Luos-Air:~ luoxiaoran$ MSEAAHVLITGAAGQIGYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPKA -bash: MSEAAHVLITGAAGQIGYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPKA: command not found Luos-Air:~ luoxiaoran$ AFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPEN -bash: AFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPEN: command not found Luos-Air:~ luoxiaoran$ FSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFKKI -bash: FSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFKKI: command not found Luos-Air:~ luoxiaoran$ GHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIHVV -bash: GHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIHVV: command not found Luos-Air:~ luoxiaoran$ EGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG* -bash: EGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG*: command not found Luos-Air:~ luoxiaoran$ Then when I try to do this (I am not sure what it is supposed to do, but have been guaranteed that it works) I get: Luos-Air:~ luoxiaoran$ cd /users/luoxiaoran/Documents/modAb101 Luos-Air:modAb101 luoxiaoran$ python3 modelAb101.py Traceback (most recent call last): File "modelAb101.py", line 2, in <module> from modeller import * # Load standard Modeller classes ModuleNotFoundError: No module named 'modeller' Luos-Air:modAb101 luoxiaoran$ I have tried troubleshooting it by downloading it via the Mac Installer instead, but that just seemed to interfere with everything so I uninstalled both versions of Modeller using brew uninstall modeller and sudo rm -rf /Library/modeller-9.24/ /usr/local/bin/mod9.24 /Library/Python/2.?/site-packages/modeller.pth /var/db/receipts/org.salilab.modeller.*, and reinstalled it using only brew install modeller. During uninstalling, I also uninstalled and reinstalled Homebrew, and manually deleted all the folders that Terminal informed me could not be deleted automatically (including the Python framework, which I later found out should never be deleted, so I reinstalled python and python(a)3.8 using both Homebrew and the official Python website's Mac Installer for Python 3.8.3) before the reinstallation of Homebrew and modeller. I also entered the modeller license key by modifying the config.py document, just as the program told me to. Do you know what's wrong, how to find out what's wrong, and/or how to solve it? Thank you so much! Best, Luna

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Re: [modeller_usage] Command not found, no module named 'modeller' errors
by Xiao Ran Luo 28 May '20

28 May '20

Thanks for your reply! Unfortunately, my Mandarin is not good enough to reply in Mandarin, sorry -do you mean I should uninstall Python 3.8.3 and install Python 2.7 or below? I did that, moved Python from Applications to Trash, and did brew uninstall python and brew uninstall python(a)3.8, then I installed Python 2.7.18 from the official website (because I can't seem to install versions below 2.7, the Installer keeps telling me that "there was no software found to install"). However, when I try to check what version of Python I am using on Terminal, I get: Luos-Air:~ luoxiaoran$ python --version Python 2.7.10 Luos-Air:~ luoxiaoran$ python3 --version Python 3.8.3 Luos-Air:~ luoxiaoran$ And the above code from my first email still does not work. On Thu, May 28, 2020 at 6:14 PM Min-yi Shen <minyishen(a)gmail.com> wrote: > Modeler 其實就是 python 裡的一模塊。讓事情複雜的是：一般的機子上還會有 python 和 python3 > 這兩個，有時這破模塊會被裝到另一個 python 下，我看你用的是 python3 版，找不到。試試 python （2.7 版）下面有沒有。 > > （註明：我現在不是 modeler 開發者了，12 年前是） > > On Thu, May 28, 2020 at 18:04 Xiao Ran Luo via modeller_usage < > modeller_usage(a)salilab.org> wrote: > >> Hello, >> >> I just downloaded version 9.24 of Modeller onto by macOS version 10.14.1 >> using Homebrew, but when I try to run the first few lines of the basic >> tutorial, I get a lot of "command not found": >> >> Luos-Air:~ luoxiaoran$ >P1;TvLDH >> >> -bash: TvLDH: command not found >> >> Luos-Air:~ luoxiaoran$ sequence:TvLDH:::::::0.00: 0.00 >> >> -bash: sequence:TvLDH:::::::0.00:: command not found >> >> Luos-Air:~ luoxiaoran$ >> MSEAAHVLITGAAGQIGYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPKA >> >> -bash: >> MSEAAHVLITGAAGQIGYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPKA: >> command not found >> >> Luos-Air:~ luoxiaoran$ >> AFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPEN >> >> -bash: >> AFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPEN: >> command not found >> >> Luos-Air:~ luoxiaoran$ >> FSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFKKI >> >> -bash: >> FSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFKKI: >> command not found >> >> Luos-Air:~ luoxiaoran$ >> GHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIHVV >> >> -bash: >> GHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIHVV: >> command not found >> >> Luos-Air:~ luoxiaoran$ EGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG* >> >> -bash: EGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG*: command not found >> >> Luos-Air:~ luoxiaoran$ >> >> >> >> Then when I try to do this (I am not sure what it is supposed to do, but >> have been guaranteed that it works) I get: >> >> Luos-Air:~ luoxiaoran$ cd /users/luoxiaoran/Documents/modAb101 >> >> Luos-Air:modAb101 luoxiaoran$ python3 modelAb101.py >> >> Traceback (most recent call last): >> >> File "modelAb101.py", line 2, in <module> >> >> from modeller import * # Load standard Modeller classes >> >> ModuleNotFoundError: No module named 'modeller' >> >> Luos-Air:modAb101 luoxiaoran$ >> >> >> I have tried troubleshooting it by downloading it via the Mac Installer >> instead, but that just seemed to interfere with everything so I uninstalled >> both versions of Modeller using brew uninstall modeller and sudo rm -rf >> /Library/modeller-9.24/ /usr/local/bin/mod9.24 >> /Library/Python/2.?/site-packages/modeller.pth >> /var/db/receipts/org.salilab.modeller.*, and reinstalled it using only brew >> install modeller. During uninstalling, I also uninstalled and >> reinstalled Homebrew, and manually deleted all the folders that Terminal >> informed me could not be deleted automatically (including the Python >> framework, which I later found out should never be deleted, so I >> reinstalled python and python(a)3.8 using both Homebrew and the official >> Python website's Mac Installer for Python 3.8.3) before the reinstallation >> of Homebrew and modeller. I also entered the modeller license key by >> modifying the config.py document, just as the program told me to. >> >> >> Do you know what's wrong, how to find out what's wrong, and/or how to >> solve it? Thank you so much! >> >> >> Best, >> >> Luna >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage(a)salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >> >

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How to properly set the fields 5 of the second line in the .aln file?
by ZHANG Cheng 21 May '20

21 May '20

I have a two-chain protein to model, Chain A and Chain B. In the PDB file, the Chain B residues are numbered from 3-33, so only 31 residues appear in the PDB. When "1 :A:+33 :B" is used for the fields 3-6 in the second line of the .aln file, I got error: "Number of residues in the alignment and  pdb files are different". When it is changed to "1 :A:+31 :B", the same error occurred. However, when only Chain B is modelled, "3 :B:+33 :B" can be run successfully. So, it seems that, when Field 5 = n, it assumes that the last chain has in total n residues, not the last residue is numberred as n. So how should I set the Field 5 number? Do I have to renumber the Chain B residues in the PDB from 1 to 31? Thank you!

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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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