May 2006 - modeller_usage

exposed core in generated structures
by Daniel Sullivan 17 May '06

17 May '06

Hello all- I have a series of models that I'm looking to analyze. It seems that in many cases, the models that have been created have surface pockets/holes exposing a small portion of the hydrophobic core that are unexpected (given the template structures) and which I believe to be artifacts to the modeling process. The alignments are good, and I've been unable to come up with a way to get rid of these holes. Any suggestions are more than welcome. I also have images that I can email if what I wrote above isn't decriptive enough.

1 0

Modelling problem
by Joydeep 16 May '06

16 May '06

Hi, I am modelling a protein 763 amino acids long. There aer no templates available for this protein to thread the sequence onto. The 3D structure of a part of the protein (1 out of 4 domains), however, has been elucidated by NMR spectroscopy. My protein also contains the well-known homeobox domain. I have tried modelling the protein using an alignment with a template obtained from mGenThreader (as shown in the difficult-example tutorial). But the structures obtained by this method show no resemblance to the homeobox domain in the region known to contain the homeobox domain. Is there a way I can incorporate these known structures along with the template obtained from mGenThreader? Please help. Thanking you Joydeep Mitra _______________________________________________ Join Excite! - http://www.excite.com The most personalized portal on the Web!

1 0

Re : modeller_usage Digest, Vol 5, Issue 63
by doppelt olivia 15 May '06

15 May '06

mais si il y a des assurances pour ça et s'il te plait, viens on essaye de bosser un peu sans y penser trop. Moi j'arrive pas à gérer. on verra bien ! Olivia Doppelt ----- Message d'origine ---- De : modeller_usage-request(a)salilab.org À : modeller_usage(a)salilab.org Envoyé le : Jeudi, 11 Mai 2006, 4h34mn 24s Objet : modeller_usage Digest, Vol 5, Issue 63 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit http://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: loop modeling limits (Modeller Caretaker) 2. Re: specify sequence ranges for salign/align2d (Modeller Caretaker) 3. ERROR: No alignment (Joydeep) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 May 2006 12:44:28 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] loop modeling limits To: lorix <Loris.Moretti(a)pharm.unige.ch> Cc: modeller_usage(a)salilab.org Message-ID: <4462429C.6050205(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed lorix wrote: > I would like to build part of a protein which is missing from the PDB file. > It is a very long loop (72 residues) and I am not sure if the task is > beyond Modeller skills. Any loop longer than 12 residues or so is going to be essentially impossible to model with this protocol - the conformational space is just too large. You should try to find other templates with reasonable sequence identity to cover at least part of this long loop. 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: Wed, 10 May 2006 12:52:11 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] specify sequence ranges for salign/align2d To: Douglas Kojetin <douglas.kojetin(a)gmail.com> Cc: modeller_usage(a)salilab.org Message-ID: <4462446B.7070505(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Douglas Kojetin wrote: > WIth reference to Tutorial 2 (Advanced Modeling): > > http://salilab.org/modeller/tutorial/advanced.html > > Is it possible to: > > (1) specify the sequence number ranges for the templates to be used in > the structural alignment within 'salign.py'? > > or > > (2) specify the sequence number ranges for the template or target to be > used in the sequence alignment within the script 'align2d_mult.py'? Of course - both of these are straightforward. For (1), just specify model_segment when you read in the model. The example you mention reads a whole chain for each PDB, but you can read whatever you like, e.g. aln = alignment(env) mdl = model(env, file='foo.pdb', model_segment=('1:', '34:')) aln.append_model(mdl, atom_files='foo', align_codes='foo') mdl = model(env, file='bar.pdb', model_segment=('3:A', '95:B')) aln.append_model(mdl, atom_files='bar', align_codes='bar') and so on... This makes an alignment of residues 1-34 from 'foo.pdb' against residues 3:A to 95:B from 'bar.pdb'. For (2), you can give the residue range in the alignment file header. See http://salilab.org/modeller/manual/node176.html. The example there reads residues 1-106 for the 5fd1 structure, and 1-54 for the 1fdx sequence. 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: 3 Date: Thu, 11 May 2006 10:23:06 -0400 (EDT) From: "Joydeep" <joy_alwayslate(a)excite.com> Subject: [modeller_usage] ERROR: No alignment To: modeller_usage(a)salilab.org Message-ID: <20060511142306.928DC99DF4(a)xprdmxin.myway.com> Content-Type: text/plain; charset="us-ascii" Hi, I'm trying to model a large protein(763 amino acids) with a distant template obtained from mGenThreader...but when i run the model.py command (as shown in tutorial), i get the following: -------------------------------------------------------------------- Type 'mod8v2' to run Modeller. C:\Modeller>mod8v2 c:\Mitra\Project_Experiments\the_align\theAlignment.top 'import site' failed; use -v for traceback C:\Modeller>mod8v2 c:\Mitra\Project_Experiments\the_align\model.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "c:\Mitra\Project_Experiments\the_align\model.py", line 9, in ? a.make() File "C:\Modeller\modlib\modeller\automodel\automodel.py", line 100, in make self.homcsr(exit_stage) File "C:\Modeller\modlib\modeller\automodel\automodel.py", line 331, in homcsr aln.check() File "C:\Modeller\modlib\modeller\alignment.py", line 153, in check io=io.modpt, libs=libs.modpt, **vars) File "C:\Modeller\modlib\modeller\util\top.py", line 37, in check_alignment return _modeller.check_alignment(aln, io, libs, *args) _modeller.error: check_a_335E> No alignment. C:\Modeller> --------------------------------------------------------------------- I checked the alignment file, it seems okay to me...so i can't figure out what's going wrong. Can someone please tell me what could possibly be wrong with the alignment? Thanks in advance Joy _______________________________________________ Join Excite! - http://www.excite.com The most personalized portal on the Web!

1 0

NO PDB
by Joydeep 12 May '06

12 May '06

Hi, I managed to run the model routine through a top file (it worked only after i specified the directory for the atom files), and the program runs without any errors, but it dosen't generate any PDB files. Isn't it supposed to generate a PDB file for each model, so that they can be evaluated? If not, how can i get the structure from the information obtained in the log file? Please help. Thanks in advance Joy _______________________________________________ Join Excite! - http://www.excite.com The most personalized portal on the Web!

2 1

CA-CA restraints
by Mensur Dlakic 11 May '06

11 May '06

Hi, Is there any way to force Modeller to generate restraints for consecutive CA atoms instead for every other one? What is the reason for excluding i, i+1 restraints for CA atoms? Thanks, Mensur ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

2 3

ERROR: No alignment
by Joydeep 11 May '06

11 May '06

Hi, I'm trying to model a large protein(763 amino acids) with a distant template obtained from mGenThreader...but when i run the model.py command (as shown in tutorial), i get the following: -------------------------------------------------------------------- Type 'mod8v2' to run Modeller. C:\Modeller>mod8v2 c:\Mitra\Project_Experiments\the_align\theAlignment.top 'import site' failed; use -v for traceback C:\Modeller>mod8v2 c:\Mitra\Project_Experiments\the_align\model.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "c:\Mitra\Project_Experiments\the_align\model.py", line 9, in ? a.make() File "C:\Modeller\modlib\modeller\automodel\automodel.py", line 100, in make self.homcsr(exit_stage) File "C:\Modeller\modlib\modeller\automodel\automodel.py", line 331, in homcsr aln.check() File "C:\Modeller\modlib\modeller\alignment.py", line 153, in check io=io.modpt, libs=libs.modpt, **vars) File "C:\Modeller\modlib\modeller\util\top.py", line 37, in check_alignment return _modeller.check_alignment(aln, io, libs, *args) _modeller.error: check_a_335E> No alignment. C:\Modeller> --------------------------------------------------------------------- I checked the alignment file, it seems okay to me...so i can't figure out what's going wrong. Can someone please tell me what could possibly be wrong with the alignment? Thanks in advance Joy _______________________________________________ Join Excite! - http://www.excite.com The most personalized portal on the Web!

2 1

specify sequence ranges for salign/align2d
by Douglas Kojetin 10 May '06

10 May '06

Hello- WIth reference to Tutorial 2 (Advanced Modeling): http://salilab.org/modeller/tutorial/advanced.html Is it possible to: (1) specify the sequence number ranges for the templates to be used in the structural alignment within 'salign.py'? or (2) specify the sequence number ranges for the template or target to be used in the sequence alignment within the script 'align2d_mult.py'? Thanks, Doug

2 1

loop modeling limits
by lorix 10 May '06

10 May '06

Dear users, I would like to build part of a protein which is missing from the PDB file. It is a very long loop (72 residues) and I am not sure if the task is beyond Modeller skills. I have information about secondary structure elements of this protein part (three helices and a strand) thus I tried to use them as restrains in the program but what I got after increasing the automodel.max_molpdf (because it did not produce any results with the default limit) was just a long flat and linear loop without any apparent secondary structure. Might be I did not check enough into the available literature about the program and there are ways to model such a loop or it is just not possible. Can someone, please, help me with a suggestion? that's the input file: # Homology modelling by the automodel class with special restrains for secondary structure from modeller.automodel import * # Load the automodel class # Redefine the special_restraints routine to include the secondary # structure restraints (this routine is empty by default): class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints # Three alpha-helix: rsr.make(aln, restraint_type='ALPHA', residue_ids=('143', '148'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids=('195', '200'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids=('204', '206'), spline_on_site=False) # One strand: rsr.make(aln, restraint_type='STRAND', residue_ids=('171', '174'), spline_on_site=False) log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './' a = mymodel(env, alnfile='protein_full.ali', # alignment filename knowns='PDB_refined', # codes of the templates sequence='protein_full') # code of the target 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.max_molpdf = 500000 # define the max of molec probability density function a.md_level = refine.fast # type of refinement of model a.make() thanks loris...

2 1

complex modelling
by Bianca Flores 09 May '06

09 May '06

I am new to modeller. I have the cristallographic complex of the proteins A and B, and I want to model the complex between A' and B, where A is the protein A but from other organism (%identity = 30%). B is the same protein. How can I do that?. I have structures of proteins very similar in sequence to A', but in te un-complexed form. Kind regards.

1 0

PDB id's found in buildtarget.py is missing in sequence database??
by Robert Selwyne 30 Apr '06

30 Apr '06

Good Day!!!!!!!!! I have a doubt, that modeller searches the best templates with respect to our target sequence in the sequence database using the command $mod8v2 buildtarget.py Now i make my comparetarget.py by adding the best five template's PDB i.d's as i got from buildtarget.log $mod8v2 comparetarget.py i get these errors!!!!!!!!!!!! ============================================================================= Traceback (most recent call last): File "compare target.py", line 7, in ? aln.malign3d() File "/usr/lib/modeller8v2/modlib/modeller/alignment.py", line 210, in malign3d io=io.modpt, libs=libs.modpt, **vars) File "/usr/lib/modeller8v2/modlib/modeller/util/top.py", line 93, in malign3d return _modeller.malign3d(aln, io, libs, *args) _modeller.error: malign3_682E> Structural information is not available for all sequences in the alignment. Aborting. ============================================================================ I am surprised to see the error -structural information is not available. It means the PDB i'ds are missing in the sequence database?. But those PDB id.s are taken from my buildtarget.log. How can i execute compare target.log? Now I have downloaded the necessary PDB files manually, Could you tell which/where directory to paste these files with a detailed command list since i am beginner to modeller. With Regards Robert Selwyne.

2 1