April 2007 - modeller_usage

Unpick restraints and partial optimization.
by Gregoire Depret 26 Apr '07

26 Apr '07

Dear Modeller users, I am trying to unselect some restraints of the restraint file coming from my homology model in order to perform some optimization. Following the recommandations, I have tried the unpick method like this. mdl = complete_pdb(env, 'homo_model.pdb') mdl.restraints.append(file='./original_restraints.rsr') mdl.rename_segments(segment_ids=('A', 'A', 'B'), renumber_residues=(32, 98, 693)) allrest = selection(mdl) mdl.restraints.pick(allrest) mdl.restraints.unpick(mdl.residue_range('706:B', '736:B')) mdl.restraints.condense() I get the following logfile runcmd______> restraints.append(file='./original_restraints.rsr') runcmd______> model.rename_segments(segment_ids=('A', 'A', 'B'), renumber_residues=(32, 98, 693)) runcmd______> restraints.pick((def)residue_span_range=(0, 99999), (def)restraint_sel_atoms=1, (def)restraints_filter={'default':-999 .000000}) runcmd______> restraints.unpick() unpick__441_> Number of restraints unselected: 0 condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 101301 101301 None of the restraints were removed. Since I renumber my model I have tried the restraint.reindex command but I didn't make it through either. I know I can edit my restraint file and remove the unwanted restraints but I can't find my residues back in the homology generated restraint file, I only read atom index. Another question. I want to perform an optimization on some parts of my model only. I have tried to add residue ranges to a selection and then optimize this selection, but in this case modeller don't take into account the unselected parts of my model and I get overlapping helices. I understand why It is happpening nevertheless is there still a way to achieve partial optimization without overlapping ? Many thanks for your answers. -- Depret Grégoire Graduate Student gdepret(a)ulb.ac.be Service de Structure et Fonction des Membranes Biologiques Centre de Biologie Structurale et de Bioinformatique Université Libre de Bruxelles Boulevard du Triomphe CP 206/2 B-1050 Bruxelles Belgium

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using multiple template in Modeller9v1
by jinlian05＠lzu.cn 19 Apr '07

19 Apr '07

Hi, I am new to modeller and I have trouble creating a homology model of a protein using multiple template. During making model,it appares model error, structure not read in.I would appreciate it if any one can give me any suggestion. Thanks! log file: runcmd______> alignment.append(align_codes=['1u19', '1PFC', '1BGY', '1AVQ', '1ARP', 'ccr'], atom_files=[], file='multiccr.ali', (def)remove_gaps=True, (def)alignment_format='PIR', (def)rewind_file=False, (def)close_file=True) readlinef__W> File: 1u19.pdb, Line: 1371 Modeller will only read the first 80 characters of this line. readlinef__W> File: 1u19.pdb, Line: 1371 Modeller will only read the first 80 characters of this line. read_pd_702E> File: 1u19.pdb, Line 1371 Could not parse data from file; file is probably corrupt. read_te_288W> Protein not accepted: 1 1u19 rdabrk__337E> Structure not read in (please consult the log file for more details):

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Rigid bodies on the backbone only.
by Gregoire Depret 18 Apr '07

18 Apr '07

Hello, I would like to apply rigid bodies only on the mainchain of my model in order to run molecular dynamics and conjuguate gradients. I have already tried to do it with : mdl.restraints.rigid_bodies.append(rigid_body(mdl.residue_range('56:A', '48:A'))) and just before the optimization start : atmselall = selection(mdl) atmsel = selection.only_mainchain(atmselall) and then : cg.optimize(atmsel, max_iterations=50, actions=actions.trace(5, trcfil)) But my model is destroyed by CG and MD which is not the case when rigid body is applied on the whole chain. Maybe I can define "rigid_body" with "atom_range" in place of "residue_range" and selecting all the atoms of the backbone (Ca, CO, N) for my residue range, but I think there must be a better way to achieve this. Many Thanks for any suggestion. Depret Grégoire Graduate Student gdepret(a)ulb.ac.be Service de Structure et Fonction des Membranes Biologiques Centre de Biologie Structurale et de Bioinformatique Université Libre de Bruxelles Boulevard du Triomphe CP 206/2 B-1050 Bruxelles Belgium

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stuck even before begining - how to create the .ali file
by Ariel Bensimon 18 Apr '07

18 Apr '07

I would like to use MODELLER to structurally align a protein domain with a known PDB. But I am stuck. I could even create the basic .ali file. Trying using the manual. Couldn't find the basic start of things Thanx , A.

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using model-addrsr in modeller9v1
by jinlian05＠lzu.cn 17 Apr '07

17 Apr '07

Hi, I am new to modeller and I have trouble creating a homology model of a protein using model-addrsr. By predicting secondary structure, between residues "305-318" is alpha-helix. I modified the model-addrsr.py script as shown below and I got error messages. I would appreciate it if any one can give me any suggestion. Thanks. 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 special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(secondary_structure.alpha(self.residue_range('305:', '318:'))) a = mymodel(env, alnfile = 'seg.ali', # alignment filename knowns = '1u19A', # codes of the templates sequence = 'mrg1') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling The error: File "modelrsr.py", line 14 rsr.add(secondary_structure.alpha(self.residue_range('305:', '318:'))) ^ IndentationError: unindent does not match any outer indentation level The .log file: MODELLER 9v1, 2007/01/19, r4822 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2007 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux linux 2.6.11.4-21.7-default i686 Date and time of compilation : 2007/01/19 13:47:34 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2007/04/17 22:15:53

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using model-loop-refine in Modeller9v1
by jinlian05＠lzu.cn 17 Apr '07

17 Apr '07

Hi, I am new to modeller and I have trouble creating a homology model of a protein using model-loop-refine. I modified the model-loop-refine.py script as shown below and I got error messages. I would appreciate it if any one can give me any suggestion. Thanks. from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files' # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('53:', '67:') (self.residue_range('89:', '96:') (self.residue_range('118:', '144:') (self.residue_range('166:', '177:') (self.residue_range('199:', '221:') (self.residue_range('243:', '254:')) a = myloop(env, alnfile = 'seg.ali', # alignment filename knowns = '1u19A', # codes of the templates sequence = 'mrg1', # code of the target loop_assess_methods=assess.DOPE) # assess each loop with DOPE a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 2 # Last loop model a.make() # do modeling and loop refinement This is the error: File "model-loop-refine.py", line 21 m = myloop(env, ^ SyntaxError: invalid syntax

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Re: [modeller_usage] using model-loop-refine in Modeller9v1
by Pankaj R. Daga 17 Apr '07

17 Apr '07

Hey jin lian I guess you need to remove the parentheses before "self.residue_range". They are not necessary or else, you need to compete those parentheses. This is not the problem of modeller, rather its mainly related to python script. hope this helps. Cheers PanDa =================================================================== If your ship doesn't come in, swim out to it.......Jonathan Winters =================================================================== Pankaj R. Daga | Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638 University of Mississippi | phone: +1-662-915-1853 University, MS, 38677-1848 | ===================================================================

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Re: [modeller_usage] using model-loop-refine in Modeller9v1
by Pankaj R. Daga 17 Apr '07

17 Apr '07

Hey jin lian I guess you need to remove the parentheses before "self.residue_range". They are not necessary or else, you need to compete those parentheses. This is not the problem of modeller, rather its mainly related to python script. hope this helps. Cheers PanDa =================================================================== If your ship doesn't come in, swim out to it.......Jonathan Winters =================================================================== Pankaj R. Daga | Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638 University of Mississippi | phone: +1-662-915-1853 University, MS, 38677-1848 | =================================================================== ----- Original Message ----- From: <modeller_usage-request(a)salilab.org> To: <modeller_usage(a)salilab.org> Sent: Tuesday, April 17, 2007 5:32 AM Subject: modeller_usage Digest, Vol 6, Issue 33 > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: Psi and Phi Dihedral Restraints (Modeller Caretaker) > 2. using model-loop-refine in Modeller9v1 (jinlian05(a)lzu.cn) > 3. Re: using model-loop-refine in Modeller9v1 (Charlie Allerston) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 16 Apr 2007 23:40:48 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] Psi and Phi Dihedral Restraints > To: Brandon Mills <bmm25(a)pitt.edu> > Cc: modeller_usage(a)salilab.org > Message-ID: <46246BF0.1030209(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Brandon Mills wrote: >> I have recently been toying with certain restraints in my .rsr files, >> and I have a couple questions. Can someone elaborate on the effect of >> restraints which contain eight atoms and a multiple of six parameters >> (I've seen 6, 12, 18, 24, and 30), and the restraints which contain 4 >> atoms and 28 parameters? What exactly are these parameters? Also, is >> there an easy way to pick out the psi and phi restraints out of the >> general dihedral restraints? Thanks in advance! > > See http://salilab.org/modeller/9v1/manual/node382.html for a > description of the restraints file format. The second column (restraint > form) is the one you're probably interested in (it will be 9 for > multi-binormal (phi/psi) restraints). There is a multiple of six > parameters for each of these because there are six parameters for each > well in the function (weight, 2 means, 2 stdevs, and a correlation; see > http://salilab.org/modeller/9v1/manual/node91.html) > > The other restraints you mention are almost certainly cubic spline > restraints (form 10). These are used because it is more efficient to > evaluate a cubic spline than a multiple Gaussian. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 2 > Date: Tue, 17 Apr 2007 16:49:01 +0800 > From: "" <jinlian05(a)lzu.cn> > Subject: [modeller_usage] using model-loop-refine in Modeller9v1 > To: modeller_usage(a)salilab.org > Message-ID: <376799741.12858(a)st.lzu.edu.cn> > Content-Type: text/plain > > Hi, > I am new to modeller and I have trouble creating a homology model of a > protein using model-loop-refine. I modified the model-loop-refine.py script as > shown below and I got error messages. I would appreciate it if any one > can give me any suggestion. > Thanks. > > from modeller import * > from modeller.automodel import * > > log.verbose() > env = environ() > > env.io.atom_files_directory = './:../atom_files' > > # Create a new class based on 'loopmodel' so that we can redefine > # select_loop_atoms > class myloop(loopmodel): > # This routine picks the residues to be refined by loop modeling > def select_loop_atoms(self): > return selection(self.residue_range('53:', '67:') > (self.residue_range('89:', '96:') > (self.residue_range('118:', '144:') > (self.residue_range('166:', '177:') > (self.residue_range('199:', '221:') > (self.residue_range('243:', '254:')) > > a = myloop(env, > alnfile = 'seg.ali', # alignment filename > knowns = '1u19A', # codes of the templates > sequence = 'mrg1', # code of the target > loop_assess_methods=assess.DOPE) # assess each loop with DOPE > a.starting_model= 1 # index of the first model > a.ending_model = 1 # index of the last model > > a.loop.starting_model = 1 # First loop model > a.loop.ending_model = 2 # Last loop model > > a.make() # do modeling and loop refinement > > This is the error: > File "model-loop-refine.py", line 21 > m = myloop(env, > ^ > SyntaxError: invalid syntax > > > > > > ------------------------------ > > Message: 3 > Date: Tue, 17 Apr 2007 10:32:29 +0000 > From: "Charlie Allerston" <charlieboyblue(a)hotmail.com> > Subject: Re: [modeller_usage] using model-loop-refine in Modeller9v1 > To: jinlian05(a)lzu.cn, modeller_usage(a)salilab.org > Message-ID: <BAY117-F1818D25C2653CF5F52AE3CDD510(a)phx.gbl> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: http://salilab.org/archives/modeller_usage/attachments/20070417/32969431/at… > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 6, Issue 33 > ********************************************* > >

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Re: [modeller_usage] using model-loop-refine in Modeller9v1
by jinlian05＠lzu.cn 17 Apr '07

17 Apr '07

Hi, I am new to modeller and I have trouble creating a homology model of a protein using model-loop-refine. I modified the model-loop-refine.py script as shown below and I got error messages. About an hour before, I got your repaly of the 'using model-loop-refine in Modeller9v1', you sent me a URL 'http://salilab.org/archives/modeller_usage/attachments/20070417/32969431/at…'. But I can not understand it. Could you explain it again for me? from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files' # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('53:', '67:') (self.residue_range('89:', '96:') (self.residue_range('118:', '144:') (self.residue_range('166:', '177:') (self.residue_range('199:', '221:') (self.residue_range('243:', '254:')) a = myloop(env, alnfile = 'seg.ali', # alignment filename knowns = '1u19A', # codes of the templates sequence = 'mrg1', # code of the target loop_assess_methods=assess.DOPE) # assess each loop with DOPE a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 2 # Last loop model a.make() # do modeling and loop refinement This is the error: File "model-loop-refine.py", line 21 a = myloop(env, ^ SyntaxError: invalid syntax This is the .log contents: MODELLER 9v1, 2007/01/19, r4822 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2007 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux linux 2.6.11.4-21.7-default i686 Date and time of compilation : 2007/01/19 13:47:34 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2007/04/17 19:12:02

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Psi and Phi Dihedral Restraints
by Brandon Mills 16 Apr '07

16 Apr '07

Hello All, I have recently been toying with certain restraints in my .rsr files, and I have a couple questions. Can someone elaborate on the effect of restraints which contain eight atoms and a multiple of six parameters (I've seen 6, 12, 18, 24, and 30), and the restraints which contain 4 atoms and 28 parameters? What exactly are these parameters? Also, is there an easy way to pick out the psi and phi restraints out of the general dihedral restraints? Thanks in advance! Sincerely, Brandon Mills -- Brandon Mills bmm25(a)pitt.edu (814) 360-1382 Lab: 338, Eberly Hall

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