- modeller_usage - salilab.org

Fwd: Regarding modelling of dimer
by Bhavik Sawhney 26 May '15

26 May '15

Dear Sir, This is your post regarding modelling of the dimer protein on dimeric template. I have done the required changes in the ali file (alignment file), do I need to change the PAP file also, because I am getting following error while running Script 4 : Number of residues in the alignment and the pdb files are different. With Regards, Bhavik Hi, If you have a dimer as template and want to model a dimer with the same organisation, you just need to include a "/" character as chain breaker in the alignment file (between your 2 monomers). I join an exemple of alignment for a dimer. On Thu, 12 Jun 2003, Difei Wang wrote: > Hi, All > > I am wondering if it is possible to model a dimer structure from a dimer > template. > I can not find anything in the manual. I tried to model each of them first and > then > put them together. However, I am not sure it is good or not for the packing in > the > contact region. Thanks for your help. > > Difei >

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prepartion input file for modeller
by m_deghan1361 20 May '15

20 May '15

Hi every body I used modeller 9.12 to create a complete pdb file, I have one qeustion: after finding a suitable template by protein blast, should I upload a complete fasta of templete to create PIR file or fasta sequence of templete resulting from blast? I am looking forward to getting your answer thanks a lot best wishes

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Modeller 9.15 release
by Modeller Caretaker 19 May '15

19 May '15

The new version of Modeller, 9.15, is now available for download! Please see the download page at http://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 9.15 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.15 is primarily a bugfix release relative to the last public release (9.14). Major user-visible changes include: # Warn if 'structureX' is mistyped in alignment file header. # The "RTF restraint not found" warning is now suppressed for the common case of failing to make a peptide bond (and the associated improper) to the next residue at the end of a chain. # Suppress making peptide bond (and the associated improper) to HETATMs unless they appear to be modified amino acids (they have a carbon CA atom). # Bundled version of HDF5 updated to 1.8.13. See the Modeller manual for a full change log: http://salilab.org/modeller/9.15/manual/node40.html If you encounter bugs in Modeller 9.15, please see http://salilab.org/modeller/9.15/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 http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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default optimization and refinement protocol
by CARLOS ARTURO CARVAJAL ARIAS 06 May '15

06 May '15

Hello. I would like to know the parameters of the default optimization and refinement protocol?. I mean, for a.library_schedule is autosched.normal and a.repeat_optimization=1, but for a.max_var_iterations, a.md_level, a.max_molpdf, what parameters are used? When the template has high sequence identity with the target, what would be the recommended level of optimization and refinement? Thanks.

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modelling part by part
by Debajyoti Dutta 06 May '15

06 May '15

Hi, The protein i want to model has 12 transmembrane helices. The topology of the protein is known from an distantly related protein structure. among the 12 transmembrane domains, 5 trnasmembrane helices structures (each helix separate PDB structure) are known determined using NMR. I wonder if it is possible to model the protein based on the hybrid method (using the structural information available). Thanks for your suggestions and help. Best Debajyoti

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can modeller9.14 build a protein with modified amino acids?
by Ming Tang 28 Apr '15

28 Apr '15

Dear Ben, I modified both the top.lib and restyp.lib in modlib fold to include the hydroxyproline information. The command line added to the restyp.lib is like this: HETATM | HYP | O | | HYP | hydroxyproline There are HYP residues indicated as HETATM in the template pdb file, and when I used a target sequence does not include O in the .ali file, I got the backbone. However, when I used a target sequence containing O in the .ali file, I got the following error: Then, I searched the archive: http://salilab.org/archives/modeller_usage/2010/msg00413.html There, you said Modeller cannot build models containing modified amino acids. If this is the case, how can modifying both the top.lib and restyp.lib to add the nonstandard amino acids information make any sense? Thanks in advance.

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How to go about refinement of multiple loops in a protein model?
by vipul＠nccs.res.in 28 Apr '15

28 Apr '15

Dear Modeller_usage members, I have made 100 models of a ~260 residue protein (enzyme) using Modeller. The model has three loop regions which have significant deviation when compared with the template structure used for modelling. the first loop is due to an insertion in the model protein's sequence(i.e. this region of 3 residues is absent in the template sequence); second loop is a 16-residue long loop located at active site cleft (a region not resolved in template) ; third loop also doesn't have information from template but is a 4-residue loop. I have the following doubts and questions: Do I need to refine all of these three loops? and should there be an order in which to refine each of these loops ( i mean, starting from N-terminus of the larger loop, etc)? Do small loops (1-5 residues) need to be refined only by the modeller script 'model-loop-tiny.py'? If yes, please explain, why? Or the regular 'loop.py' script is fine? Thanks in advance, Vipul

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restyp.lib modification error
by Ming Tang 27 Apr '15

27 Apr '15

Dear modeller users, I modified the top.lib to include the information of HYP, and added the following line in restyp.lib. HETATM | HYP | O | | HYP | hydroxyproline But when I execute the align2d.py, I got the following error message: Date and time of compilation : 2014/07/30 10:34:01 MODELLER executable type : i386-w32 Job starting time (YY/MM/DD HH:MM:SS): 2015/04/27 21:32:10 map_res_217E> Single-character residue type - is not a standard residue type (one of the first 21 residues in restyp.lib). read_re_255E> PDB residue type unrecognized: BLK Traceback (most recent call last): File "C:\Users\tangm5\Downloads\basic-example\molecule\align2d - Copy.py", line 3, in <module> env = environ() File "C:\Program Files (x86)\Modeller9.14\modlib\modeller\environ.py", line 45, in __init__ self.libs = Libraries(self._restyp_lib_file, self._rand_seed) File "C:\Program Files (x86)\Modeller9.14\modlib\modeller\libraries.py", line 21, in __init__ self.__read_libs() File "C:\Program Files (x86)\Modeller9.14\modlib\modeller\libraries.py", line 26, in __read_libs _modeller.mod_libraries_read_libs(self.modpt, fh.file_pointer) _modeller.ModellerError: read_re_255E> PDB residue type unrecognized: BLK If I only modify the top.lib, it won't come out this error and can run smoothly. Could anybody give me any suggestions about what's wrong with my modification? Thanks in advance.

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DOPE score based model selection
by vipul＠nccs.res.in 20 Apr '15

20 Apr '15

Dear Modeller_usage members, Is it necessary to select the best protein model based on DOPE scores? I have made 100 models of a ~260 residue protein (enzyme) using Modeller. Then I chose the best model based on the DOPE Score and did loop refinement on a 16-residue long loop (50 refined models created) located at active site cleft. In loop-refined model the loop occludes the active site cleft, but in another loop-refined model (with intermediate DOPE score) it is alright. Can I use this loop-refined model? Also, is it essential to refine the loop even when some initial Models have good conformations of the loop? Any suggestions would be very helpful. Thanks in advance, Vipul

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Error :Too many neighbors; overflow ignored:
by Stroebel D 17 Apr '15

17 Apr '15

Hi, I am currently building a model of a protein complex. My models (automodel) were working fine. Trying to improved the input (introducing missing atoms, chain breaks, new multitemplate...) I got stuck with a log file finishing like this: " make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 20567746 20085.689 19.615 openf___224_> Open ${MODINSTALL9v14}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v14}/modlib/mnch1.mdt neighs__292W> Too many neighbors; overflow ignored: 51 50 neighs__292W> Too many neighbors; overflow ignored: 51 50 " ...The last line being repeated as if it was the output of an infinite loop. I guess my alignement and pdb are good because they have worked previously and if any misalignment is present, the error messages should appear before the ini file is created. My .py has nothing special. (see at the end of this message.) The program created the .ini, but not the .rsr file. The .ini files looks ok unless for one thing: I was surprised that the missing atoms in the file are still represented as 'missing' in the ini output. example: "ATOM 23557 CG GLN J2975 9998.0019998.0019998.001 0.00 99.99 C " Shouldn't the remaining unknown coordinates having been rebuild using internal coordinates from the Charmm topology library BEFORE the writing of the ini file? (it may be an unrelated issue...) (The Ini file also contains: SSBOND lines at the beginning and CONECT lines at the end) I come to you since I didn't find anything usefull to explain this error. If you have any idea where it could come from, I would be very gratefull if you could share it! Thanks in advance. David my.py : " from modeller import * from modeller.automodel import * # Load the automodel class from modeller import soap_protein_od log.verbose() # directories for input atom files env = environ() env.io.atom_files_directory = ['.','../atom_files'] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms a = MyModel(env, alnfile = 'AllAlignfinal.ali' , # alignment filename knowns = ('TMD', 'TMD2', 'TMD3', 'TMD4') , # codes of the templates sequence = 'TMDRat' , # code of the target assess_methods = (assess.DOPE, soap_protein_od.Scorer() )) a.starting_model= 1 # index of the first model a.ending_model = 3 # index of the last model # (determines how many models to calculate) a.md_level = refine.fast a.make() # do homology modelling " I let the "special restraints" definition because I may have to use it for an other modelling step, but it has no use here. (and it is not involved in my problem - tested) Please note that I give you here a multi-template model building (on multichain template), but adjusting the file to a single template gives the same error message. The "soap library" is also (of course) not involved (tested). (Sorry, I first send this message to "modeller-care", but obviously it is more a problem of "usage".)

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