- modeller_usage - salilab.org

Could modeller change query position in result pdb file?
by jb ZHOU 20 Feb '19

20 Feb '19

Dear Modeller creators, Hello, Modeller is one of state-of-the-art homology modeling software and I have already used several years to model three-dimensional structures. Recently, I have a question about modeller result file (pdb file). I would like to use an example to illustrate my question. I used Modeller to model a sequence in UniProt (UniProt Accesion: Q04721), and I only used parts of sequence to model (from 414 to 532), and I want to get the final three-dimensional structures file (pdb file) which the first amino acid number still start with 414 and the last amino acid number is 532. But in fact the first amino acid number in the final pdb file start with 1 (see figure below, GLU's position is 1, but it is 414 in UniProt,). I could write a script to map it manually, but it is very inconvenience, so could modeller (or module in modeller) realize this ? Sincerely, Zhoujb

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DOPE vs molpdf
by Pawel Kedzierski 11 Feb '19

11 Feb '19

Dear Modeller creators and users, I wonder, which of the scoring functions available in Modeller is preferable to choose best models. A similar question was answered back in 2006: https://salilab.org/archives/modeller_usage/2006/msg00214.html but it was related to very different use case (template of very low identity), and the answer omits the relation to molpdf. The modeller documentation on DOPE score and the 2006 DOPE paper say, that it was designed to choose the best model. However, this value is not printed out by default neither appear in the detailed evaluation of local model problems presented in the tables of restraints violations. The fact that molpdf only is selected as the default score of model quality makes DOPE at little suspicious. I mean, it looks like there was a reason to hide it. In my case, my models are good enough to all have GA341 scores equal to 1, what makes this value useless. Still, molpdf and DOPE do not correlate, so which one shall I consider more important for model choice? I see from my experience that molpdf is rather sensitive to the choice of templates (e.g. the same protein template from X-ray vs NMR can give very different molpdf values of models, with much more restraint violations for NMR). Also, if one is using multiple templates for the same sequence, the molpdf values are closer to ones obtained using single worst template than to using the best one, while DOPE values do not change much. These observations would count against relying on molpdf, but if molpdf is misleading, then the entire verbose analysis of restraint violations from which molpdf is calculated must be equally misleading. Could you share your insight and comments? With regards, Paweł Kędzierski

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Chain ID not output as part of SSM option to model.write_data
by dms305 18 Jan '19

18 Jan '19

Hi, As part of my use of Modeller, I would like to access the secondary structure information for the model. This looks to be achieved using the SSM option to model.write_data, but this produces a file which doesn’t contain the chain identifier. This could be worked around using the first column (integer index) of the file and knowledge of the chains in the PDB, but it seems awkward to have to do this when the PSA option to write_data is able to include the chain identifier. Is there an alternative way to access the secondary structures, or could this be fixed in Modeller to make using write_data easier? Thanks in advance, Daniel

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Modeller 9.21 release
by Modeller Caretaker 11 Dec '18

11 Dec '18

A new version of Modeller, 9.21, 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 9.21 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.21 adds support for Python 3.7 and contains a number of bug fixes. See the Modeller manual for a full change log: https://salilab.org/modeller/9.21/manual/node40.html If you encounter bugs in Modeller 9.21, please see https://salilab.org/modeller/9.21/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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How to (partially) override model.patch_ss_templates() ?
by Luca Jovine 28 Nov '18

28 Nov '18

Hello, I am trying to make a model of a disulfide-bonded protein, where some disulfides are the same as in my templates, but some are shuffled. I redefined the shuffled disulfides as described here: https://salilab.org/modeller/9v7/examples/automodel/model-disulfide.py but the models that I get always show the same exact disulfide connectivity of the templates, i.e. redefining special_patches does not seem to override model.patch_ss_templates(). Is there a way to achieve this, so that I can keep some conserved disulfides from my templates but change others? Thanks, Luca ------------------------------------------------------------------------ Luca Jovine, Ph.D. Professor of Structural Biology & EMBO Member Karolinska Institutet Department of Biosciences and Nutrition & Center for Innovative Medicine Medicinaren 25 Neo Blickagången 16, SE-141 83 Huddinge, Sweden E-mail: luca.jovine(a)ki.se<mailto:luca.jovine@ki.se> W3: http://jovinelab.org ------------------------------------------------------------------------ När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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Modeller license key
by Kimia Sh 14 Oct '18

14 Oct '18

please give me modeller license key.

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Installation on Ubuntu 18.04
by Marco Sette 21 Sep '18

21 Sep '18

Dear all, I'm installing Modeller 9.20 on a Ubuntu 18.04.1 LTS. Following the instructions sudo env KEY_MODELLER=myprivatekey dpkg -i modeller_9.20-1_amd64.deb myprivatekey is my access key) I get a message in which it reads, extracts and configures the software But no files or directories are created... Thanks for your help, Marco

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Usage question - specifying secondary structure and so on
by Marko Sever 04 Sep '18

04 Sep '18

So I'm using the Chimera interface to Modeller and i'm slightly modifying the script that comes with Chimera to specify the secondary structure of my target...The biggest problem I'm seeing is that helices strands and loops which dont have a template structure to align to (since the similairty is 60% and the identity is 30%) are just floating in space, they are not in a "natural" position. How do I fix that first? Secondly maybe it even is accepting the secondary structure restraint, but it is severly beding the helices, since it wants to aggresivly align to the template structure...with which parameters would I handle this so I could get a reasonable structure? I'm inputing below the script that I'm using. Thanks for the help! Mark # --- UCSF Chimera Copyright --- # Copyright (c) 2000 Regents of the University of California. # All rights reserved. This software provided pursuant to a # license agreement containing restrictions on its disclosure, # duplication and use. This notice must be embedded in or # attached to all copies, including partial copies, of the # software or any revisions or derivations thereof. # --- UCSF Chimera Copyright --- # This script is generated by the Modeller Dialog in Chimera, # incorporating the settings from the user interface. User can revise # this script and submit the modified one into the Advanced Option panel. # Import the Modeller module 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): rsr = self.restraints at = self.atoms rsr.add(secondary_structure.strand(self.residue_range('1:', '26:'))) rsr.add(secondary_structure.alpha(self.residue_range('27:', '50:'))) rsr.add(secondary_structure.strand(self.residue_range('51:', '62:'))) rsr.add(secondary_structure.alpha(self.residue_range('63:', '88:'))) rsr.add(secondary_structure.strand(self.residue_range('89:', '100:'))) rsr.add(secondary_structure.alpha(self.residue_range('101:', '127:'))) rsr.add(secondary_structure.strand(self.residue_range('128:', '136:'))) rsr.add(secondary_structure.alpha(self.residue_range('137:', '162:'))) rsr.add(secondary_structure.strand(self.residue_range('163:', '174:'))) rsr.add(secondary_structure.alpha(self.residue_range('175:', '201:'))) rsr.add(secondary_structure.strand(self.residue_range('202:', '204:'))) rsr.add(secondary_structure.alpha(self.residue_range('205:', '226:'))) rsr.add(secondary_structure.strand(self.residue_range('227:', '276:'))) rsr.add(secondary_structure.alpha(self.residue_range('277:', '303:'))) rsr.add(secondary_structure.strand(self.residue_range('304:', '312:'))) rsr.add(secondary_structure.alpha(self.residue_range('313:', '340:'))) rsr.add(secondary_structure.strand(self.residue_range('341:', '376:'))) rsr.add(secondary_structure.alpha(self.residue_range('377:', '400:'))) rsr.add(secondary_structure.strand(self.residue_range('401:', '420:'))) rsr.add(secondary_structure.alpha(self.residue_range('421:', '450:'))) rsr.add(secondary_structure.strand(self.residue_range('451:', '457:'))) rsr.add(secondary_structure.alpha(self.residue_range('458:', '483:'))) rsr.add(secondary_structure.strand(self.residue_range('484:', '485:'))) rsr.add(secondary_structure.alpha(self.residue_range('486:', '510:'))) rsr.add(secondary_structure.strand(self.residue_range('511:', '525:'))) rsr.add(secondary_structure.alpha(self.residue_range('526:', '551:'))) rsr.add(secondary_structure.strand(self.residue_range('552:', '638:'))) rsr.add(secondary_structure.alpha(self.residue_range('639:', '664:'))) #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() # ---------- Accesing output data after modeling is complete ---------- # Get a list of all successfully built models from a.outputs if loopRefinement: ok_models = filter(lambda x: x['failure'] is None, a.loop.outputs) else: ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by index number #key = 'num' #ok_models.sort(lambda a,b: cmp(a[key], b[key])) def numSort(a, b, key="num"): return cmp(a[key], b[key]) ok_models.sort(numSort) # Output the list of ok_models to file ok_models.dat fMoutput = open('ok_models.dat', 'w') fMoutput.write('File name of aligned model\t GA341\t zDOPE \n') for m in ok_models: results = '%s\t' % m['name'] results += '%.5f\t' % m['GA341 score'][0] results += '%.5f\n' % m['Normalized DOPE score'] fMoutput.write( results ) fMoutput.close() Marko Sever, mag.farm. Doktorski študent / PhD student [KI] [KI] Teoretični odsek / Theory Department Kemijski inštitut / National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenija / Slovenia Telefon / Phone: 00386 1 476 0 408 marko.sever(a)ki.si<mailto:%20marko.sever@ki.si> <mailto:%20marko.sever@ki.si> www.ki.si<http://www.ki.si/>

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Creating a threaded protein template?
by Ahmad Khalifa 27 Aug '18

27 Aug '18

Hello, I want to create a threaded template without building the nonaligned region? is it possible using modeller? How can I modify the code here to do so? https://salilab.org/modeller/tutorial/basic.html Regards.

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Alignment format in fasta
by Ahmad Khalifa 27 Aug '18

27 Aug '18

Can I get an alignment in fasta format between two proteins using modeller? Can I convert the pir or par format to fasta? Regards.

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