modeller_usage

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3151 discussions

Superposition Problem
by Christopher Mohr 23 Jun '09

23 Jun '09

Dear Modellers, is there the possibility to create a representation of the superposition of two proteins in MODELLER? I've used the following example script to create the superposition of the two proteins: Example: examples/commands/superpose.py # Example for: selection.superpose() # This will use a given alignment to superpose Calpha atoms of # one structure (2ctx) on the other (1fas). from modeller import * env = environ() env.io.atom_files_directory = ['../atom_files'] mdl = model(env, file='1fas') mdl2 = model(env, file='2ctx') aln = alignment(env, file='toxin.ali', align_codes=('1fas', '2ctx')) atmsel = selection(mdl).only_atom_types('CA') r = atmsel.superpose(mdl2, aln) # We can now use the calculated RMS, DRMS, etc. from the returned 'r' object: rms = r.rms drms = r.drms print "%d equivalent positions" % r.num_equiv_pos mdl2.write(file='2ctx.fit') Do I have to use the outputed *.fit file to create a representation (*.pdb file for example) or is there any other possibility to create a representation to actually see the superpositioned structures of the proteins ? Thanks Christopher

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iterative_structural_align question
by Mike White 18 Jun '09

18 Jun '09

I noticed that 9v7 has a new command that is designed to obtain the best set of parameters (gap_penalties_1d and gap_penalties_3d) for aligning two or more structures. Since the reference (Madhusudhan et al 2009) is not yet available, I had a few questions based on trying the command. (1) Based on the output log, the first parameter of gap_penalties_1d is varied from -150 to 0, and the second is varied from -50 to 0. The default values for gap_penalties_1d in for alignment.salign() are (-900, -50). What is the logic for the choice of ranges for gap_penalties_1d values in iterative_structural_align()? I always assumed that the default values of the various parameters in alignment.salign() represent a good starting point for these values. (2) I assume that the value "final max quality" equivalent to "QUALITY_SCORE(percentage)" in the standard output of alignment.salign(). Is this correct? (2) In the Advanced Tutorial the example script "multiple_template/ salign.py" runs salign multiple times to first get a rough alignment and then refines it by incorporating more information through changes in feature_weights. Is feature_weights fixed at (1, 0, 0, 0, 0, 0) in iterative_structural_align()? If so, is there any way to use iterative_structural_align() in a manner similar to that shown in the tutorial? Thanks!

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MODELLER BASIC HELP
by bharat lal 18 Jun '09

18 Jun '09

I am recently started working with modeller .. and I have queries about it :- 1) It's written in the manual that the sequences should be in PIR format .. but for the template sequence I am not getting the second line , about the structure ?? from where I can get it ?? and whats the actual way for obtaining PIR sequences and with the structure details required as required for the template?? 2)How to align the two sequences in PIR foramat .. since I aligned the sequences in FASTA format I am not getting the same structure given in the manual as an example ?? 3) Where do I have to save the .pdb file of the template in modeller and the code that is given for homology modeling , there is nothing mentioned about the .pdb file being used ?? PLS HELP ICC World Twenty20 England '09 exclusively on YAHOO! CRICKET http://cricket.yahoo.com

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restraints loosed after loop refinement
by mario ciappy 18 Jun '09

18 Jun '09

Dear All, I have a problem with restraints after loop refeinement, in particular the distances between some atoms do not respect the restraint values set up. These values are respected after model building (without a slow MD) but not after loop refinements. I didn't use any refinement of imput model. I show the used scripts: This is for automodel: from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['NZ:114'], at['OD1:288']), mean=2.6, stdev=0.1)) rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['NE:136'], at['OD1:260']), mean=2.6, stdev=0.3)) a = MyModel (env, alnfile='allinea.pir', knowns='AB, BC', sequence='CD') a.starting_model = 1 a.ending_model = 1 a.md_level = refine.very_fast a.make() This is for loop refinement: log.verbose() env = environ() a = loopmodel(env, alnfile = 'allinea.pir', # alignment filename knowns = ''AB, BC', # codes of the templates sequence = 'CD') # 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. md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() Thank you very much in advance Mario

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Modeller 9v7 release
by Modeller Caretaker 16 Jun '09

16 Jun '09

The new version of Modeller, 9v7, 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 9v7 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v7 is primarily a bugfix release relative to the last public release (9v6). Major user-visible changes include: # A new method alignment.get_suboptimals() allows the suboptimal alignment file generated by alignment.salign() to be easily parsed. # A new method iterative_structural_align() provides a straightforward way to obtain the best SALIGN structure-structure alignment. # alignment.append() and alignment.read_one() now take a new argument, allow_alternates, which allow for alternate matches of one-letter codes when reading PIR sequence ranges from PDB files (B to N, Z to Q). # Parallel jobs have a new method, job.yield_tasks_unordered(), which is like job.run_all_tasks() but which returns results as they are generated rather than when all the tasks have finished. # Parallel jobs now default to trying to duplicate the current Python environment (using modslave.py and modpy.sh if necessary) when setting modeller_path, rather than running the mod9v7 script, since the latter may conflict with the Python version of the master. See the Modeller manual for a full change log: http://salilab.org/modeller/9v7/manual/node38.html If you encounter bugs in Modeller 9v7, please see http://salilab.org/modeller/9v7/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 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

1 0

Modeller output directory
by Riadh HAMMAMI 16 Jun '09

16 Jun '09

Hello, I have a problem concerning the output directory in modeller. I’m running script from different location (“mod9v6 /script/location/model-full.py”). The generated models (including other files) are located in the running folder. I would like to set the output directory to a fixed location (for e.g. the same of the script “/script/location/”). is there any issue ? Thank you for your help, Riadh

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problem with hetrotetrameric protein
by subarna thakur 02 Jun '09

02 Jun '09

Hello I facing a problem for building a model of a hetrotetrameric protein with 4 chain. Chain A and C are similar and have 423 aminoacids while chain B and D have 504 amino acids. The template I am taking is also a hetero tetrameric protein. Can any body please tell me how to write the header of the alignment file of the template as well as my target protein. The example given in the manual isnt quite helpful as it shows the case where there is just two chain. Subarna Thkur Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/

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(no subject)
by subarna thakur 29 May '09

29 May '09

Hi I am using the model-ligand.py script. My protein in multi-chained, do I have to make changes in the header of the aligenment file? I have put (.) sign at the end of the alignment file and also made option env.io.hetatm is set to True but when I am running the model-ligand.py, a error is coming that there is a mismatch between the alignment and PDB. Subarna Thakur Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/

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how add FE-S cluster in PDB
by subarna thakur 29 May '09

29 May '09

Dear User My template has a ligand of Fe-S cluster but when I am generating my PDB file based on this template, it is without any metal ligand..I want to know how do I incorporate the metal cluster in correct position in my PDB file. Subarna thakur Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com

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Re: [modeller_usage] loop refining of a multi chain protein
by subarna thakur 29 May '09

29 May '09

Dear Sir Thanks for suggestion ,it worked. After running the script two PDB files are generated one with extension .BL00010001 and other with .IL00000001 extension.Which one should I select and on which basis? ________________________________ From: Dinesh Babu KR <kr.dineshbabu(a)gmail.com> To: subarna thakur <thakur.subarna(a)yahoo.co.in> Sent: Friday, 29 May, 2009 11:51:19 AM Subject: Re: [modeller_usage] loop refining of a multi chain protein hi in the loop script file you have to mention the chain like this self.residue_range('77:B', '80:B') regards, dinesh On Fri, May 29, 2009 at 1:49 PM, subarna thakur <thakur.subarna(a)yahoo.co.in> wrote: Dear User I have a protein with multichain and I am using loop.py script for refining a protein but a error is coming which suggests that it fails to indentify the metioned residues in pdb file. But when I am running the same loop.py script with a alignment file and PDB file without mentioning any chain, it seems to run ok.. In case of multichain proteins what should be the changes made to the loop.py script for loop refining and how the residues should be mentioned in the script. Subarna thakur ________________________________ Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com

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