- modeller_usage - salilab.org

weighting restraints
by meier＠lmb.uni-muenchen.de 04 May '10

04 May '10

Hi, having multiple templates, I want to weight template based restraints down with respect to other (stereochemical) restraints. Is it then more sensible to weight down the template based restraints (weight < 1, weight=1 for rest) or to weight up the other restraints (weight > 1, weight=1 for rest)? Does it make any difference for the (simulated annealing) optimization scheme (because the "scale" is changed)? Thanks a lot for any hint Armin Meier

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Modeling Circular Permutations
by Spencer Bliven 04 May '10

04 May '10

Hello, I have produced a number of circular permutations for IL-1b. There are several structures available for the wild type protein, so I would like to model how the circular permutation effects the structure. Is MODELLER able to process circular permutations? If so, how would I encode this in my alignment file? It doesn't seem like the PIR format is well suited to this. Thanks in advance for your advice to a new modeller user. -Spencer Bliven

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Opening files
by pbonar＠ualberta.ca 04 May '10

04 May '10

Hi, I am new to modeller, and very inexperienced in python. I am trying to complete the first tutorial and I keep getting this error: IOError: openf______E> Cannot open file pdb_95.pir: No such file or directory. I have downloaded and extracted the files needed for this tutorial, however from what I gather by this message, the program cannot find/or read these files. Is there somewhere special where I must save them, or some other name that I have to give them. Do I have to do something to the file in order for it to work. And if so what program do I download to read the file? Thank you for you help Pam

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template quality selection criteria
by Thomas Evangelidis 28 Apr '10

28 Apr '10

Apart from sequence similarity to the target sequence and crystallographic resolution, someone told me I should also look to the electron density map info. Yet his english is not good and I haven't found yet the parameter he's referring to. Can anyone clarify what other parameters I should look to in order to select the best templates for modelling? thanks, Tom

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Modeller 9v8 release
by Modeller Caretaker 27 Apr '10

27 Apr '10

The new version of Modeller, 9v8, 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 9v8 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v8 is primarily a bugfix release relative to the last public release (9v7). Major user-visible changes include: # Silicon Graphics (IRIX) binaries are no longer provided. If you wish to use Modeller on an IRIX machine, please use the older 9v7 version. # Residues treated as BLK no longer have to be HETATM residues; they will be marked as ATOM if so defined in restyp.lib or in the template PDB (for example, DNA or RNA residues). automodel.nonstd_restraints() now builds restraints on both HETATM and BLK residues. # Bonds between BLK residues are now detected by a simple distance criterion and are restrained more strongly than other distances by automodel.nonstd_restraints(). # A new method Chain.join() allows chain breaks between chains to be removed. # Files compressed with 'xz' can now be read, provided that the 'xz' binary is available on your system. # The allow_alternates option to alignment.append() will now allow G in the alignment sequence to match any non-standard residue type in the PDB file which maps to G. This is useful if the alignment sequence is 'cleaned' as by sequence_db.read(). See the Modeller manual for a full change log: http://salilab.org/modeller/9v8/manual/node38.html If you encounter bugs in Modeller 9v8, please see http://salilab.org/modeller/9v8/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

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align3d.py
by saibal das 27 Apr '10

27 Apr '10

Dear modeller users, i have been trying to use the align3d.py script for modeller created homology model pdb files but is not working but is working for all pdb entries. is there any solution to this problem.

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Re: [modeller_usage] Alignment errors model not running
by Daniel Fernandez 27 Apr '10

27 Apr '10

sorry i forgot to attach the target sequence... it's the fasta sequence of the 1ATG protein... On Mon, Apr 26, 2010 at 8:19 PM, Daniel Fernandez <dfernan(a)gmail.com> wrote: > Hi, > > Please help me with this error. I have been more than a week trying to > solve this issue and I still can't solve it. > > Let me explain my approach to use modeller. > > 1. First I search for templates against the pdb database > 2. I select as templates the one with low e-value and reasonable > similarity percentage > 3. I use clustalW (or TCoffee) to align the target and the selected > templates. > 4. I use modeller to model the target based on the TCoffee alignment > file and the PDB files. > > I do the whole pipeline but modeller works for some sequences but for most > of them it gives me the following error and at this point I am clueless on > how to solve it. Here I attach my input files to modeller in case someone > wants to take a look at them and help me solve this issue. > > INPUT: finalseq.pir (as in modeller format, i tried all different formats > here, I attach my last approach that was to only save PDB files with the > data from a specific chain...) > template PDB files (the PDB files with the actual chain) > target.fasta > > OUTPUT: error: > get_ran_648E> Alignment sequence not found in PDB file: 3 > 2H5Y_A.pdb > (You didn't specify the starting and ending residue numbers > and > chain IDs in the alignment, so Modeller tried to guess these > from > the PDB file.) > Suggestion: put in the residue numbers and chain IDs (see the > manual) and run again for more detailed diagnostics. > You could also try running with allow_alternates=True to > accept > alternate one-letter code matches (e.g. B to N, Z to Q). > Traceback (most recent call last): > File "testclean.py", line 18, in <module> > a.make() # do the homollogy modelling > File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line > 98, in make > self.homcsr(exit_stage) > File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line > 411, in homcsr > aln = self.read_alignment() > File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line > 401, in read_alignment > aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) > File "/n/sw/modeller-9v7/modlib/modeller/alignment.py", line 79, in > append > allow_alternates) > _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not found > in PDB file: 3 2H5Y_A.pdb (You didn't specify the starting and > ending residue numbers and chain IDs in the alignment, so Modeller tried to > guess these from the PDB file.) Suggestion: put in the residue numbers and > chain IDs (see the manual) and run again for more detailed diagnostics. You > could also try running with allow_alternates=True to accept alternate > one-letter code matches (e.g. B to N, Z to Q). > > I am completely clueless on where to look the starting and ending residue > numbers and chain IDs in the alignment, clustalW does not give me that > information at all so not sure where to look that info and if possible with > the approach I am using... > > Thanks, > > Daniel F. > -- Daniel F. Department of Statistics, Harvard University 1 Oxford Street, Cambridge, MA 02138

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gaps in template alignment to query sequence in case of multidomain modelling
by saibal das 26 Apr '10

26 Apr '10

dear modeller users, i have created a multi domain model using modeller FAQ first method aligning each template to query sequence and arranging them in PIR format in multi alignment file. but template is not available for a large C terminal region of the model. Even template alignment to query has gap regions between each domains.The model is giving poor stereochemical properties. is there any solution to this problem. thanking you saibal das m.sc bioinformatics BIT mesra India.

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update profile database for PDB
by Knut J Bjuland 24 Apr '10

24 Apr '10

How can I acces ans update the pdb seqeunce database or profile database to the current database in www.pdb.org Best regards Knut J

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phi/psi angle restraint
by Armin Meier 23 Apr '10

23 Apr '10

Hi, I encountered a strange behavior, I dont understand yet. First, I replaced Modeller generated phi/psi dihedral constraints (group 25, physical.phi_psi_dihedral) in the rsr-file. In the corresponding cuser_form.c file, I get the phi and psi angle like this (in myform_eval): float phi = feat[0]; float psi = feat[1]; printf("phi=%f, psi=%f\n", phi, psi); Then Modeller is called. When comparing the printed phi/psi angles, I expected the very first ones (i.e. the first ones printed into the log-file, right at the start of optimization) to be the same as the phi/psi angles extracted from the *.ini file, because this is the starting point. But this isnt at all what I see. I hope, my description was clear enough Armin Meier

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