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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 69
by Ashish Runthala 20 Jun '12

20 Jun '12

Dear Austin, align_codes include PDB_ID + Chain_ID. So include 2vqj with its Chain_ID. Good Luck, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Wednesday, June 20, 2012 9:41:18 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 69 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: Align Code Error (Ignacio Ibarra) ---------------------------------------------------------------------- Message: 1 Date: Wed, 20 Jun 2012 12:11:16 -0400 From: Ignacio Ibarra <ibarra.ignacio(a)gmail.com> To: Austin Baker <asb93(a)pitt.edu> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] Align Code Error Message-ID: <CAHQkVidqJvn_t3NFFN-snJcVM_PNgFNsy1DR7mDOrppB01KdTQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" #the lines that generates your error aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj') Check that you have declared the code "2vqj" after some of the "P1>;" statements in the file HDAC9a_Cat.ali (i.e. ">P1;2vqj"). If MODELLER does not find it, then it is missing or not typed properly. Cheers, Ignacio On Wed, Jun 20, 2012 at 11:24 AM, Austin Baker <asb93(a)pitt.edu> wrote: > I am trying to run a 2d align and I keep getting this error. I can't seem > to figure out what the problem is. > > ERROR GENERATED: > Traceback (most recent call last): File "align2d_HDAC9a_Cat.py", line 12, > in <module> aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj') File > "/Library/modeller-9.10/modlib/modeller/alignment.py", line 78, in append > allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified > in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = > 2vqj > > SCRIPT I'M USING > # Demonstrating ALIGN2D, aligning with variable gap penalty > > from modeller import * > log.verbose() > env = environ() > > env.libs.topology.read('$(LIB)/top_heav.lib') > env.io.atom_files_directory = ['./atom_files'] > > # Read aligned structure(s): > aln = alignment(env) > aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj') > aln_block = len(aln) > > # Read aligned sequence(s): > aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj') > > # Structure sensitive variable gap penalty sequence-sequence alignment: > aln.align2d(overhang=0, gap_penalties_1d=(-100, 0), > gap_penalties_2d=(3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0., 0.), > align_block=aln_block) > > aln.write(file='align2d.ali', alignment_format='PIR') > aln.write(file='align2d.pap', alignment_format='PAP', > alignment_features='INDICES HELIX BETA STRAIGHTNESS ' + \ > 'ACCESSIBILITY CONSERVATION') > aln.check() > > # Color the first template structure according to gaps in alignment: > aln = alignment(env) > aln.append(file='align2d.ali', align_codes=('HDAC9a_Cat', '2vqj'), > alignment_format='PIR', remove_gaps=True) > mdl = model(env) > mdl.read(file=aln['HDAC9a_Cat'].atom_file, > model_segment=aln['HDAC9a_Cat'].range) > mdl.color(aln=aln) > mdl.write(file='HDAC9a_Cat.aln.pdb') > > # Color the first template structure according to secondary structure: > mdl.write_data(file='HDAC9a_Cat', output='SSM') > mdl.write(file='HDAC9A_Cat.ssm.pdb') > > # Superpose the target structure onto the first template: > mdl2 = model(env) > mdl2.read(file=aln['2vqj'].atom_file, > model_segment=aln['2vqj'].range) > sel = selection(mdl).only_atom_types('CA') > sel.superpose(mdl2, aln) > mdl2.write(file='2vqj.fit.pdb') > > > > Austin Baker > asb93(a)pitt.edu > Graduate Student > Department of Chemistry > University of Pittsburgh > > *Everything is Experimental* > > > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >

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Align Code Error
by Austin Baker 20 Jun '12

20 Jun '12

I am trying to run a 2d align and I keep getting this error. I can't seem to figure out what the problem is. ERROR GENERATED: Traceback (most recent call last): File "align2d_HDAC9a_Cat.py", line 12, in <module> aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj') File "/Library/modeller-9.10/modlib/modeller/alignment.py", line 78, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 2vqj SCRIPT I'M USING # Demonstrating ALIGN2D, aligning with variable gap penalty from modeller import * log.verbose() env = environ() env.libs.topology.read('$(LIB)/top_heav.lib') env.io.atom_files_directory = ['./atom_files'] # Read aligned structure(s): aln = alignment(env) aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj') aln_block = len(aln) # Read aligned sequence(s): aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj') # Structure sensitive variable gap penalty sequence-sequence alignment: aln.align2d(overhang=0, gap_penalties_1d=(-100, 0), gap_penalties_2d=(3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0., 0.), align_block=aln_block) aln.write(file='align2d.ali', alignment_format='PIR') aln.write(file='align2d.pap', alignment_format='PAP', alignment_features='INDICES HELIX BETA STRAIGHTNESS ' + \ 'ACCESSIBILITY CONSERVATION') aln.check() # Color the first template structure according to gaps in alignment: aln = alignment(env) aln.append(file='align2d.ali', align_codes=('HDAC9a_Cat', '2vqj'), alignment_format='PIR', remove_gaps=True) mdl = model(env) mdl.read(file=aln['HDAC9a_Cat'].atom_file, model_segment=aln['HDAC9a_Cat'].range) mdl.color(aln=aln) mdl.write(file='HDAC9a_Cat.aln.pdb') # Color the first template structure according to secondary structure: mdl.write_data(file='HDAC9a_Cat', output='SSM') mdl.write(file='HDAC9A_Cat.ssm.pdb') # Superpose the target structure onto the first template: mdl2 = model(env) mdl2.read(file=aln['2vqj'].atom_file, model_segment=aln['2vqj'].range) sel = selection(mdl).only_atom_types('CA') sel.superpose(mdl2, aln) mdl2.write(file='2vqj.fit.pdb') Austin Baker asb93(a)pitt.edu Graduate Student Department of Chemistry University of Pittsburgh Everything is Experimental

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energy function
by Armin Meier 12 Jun '12

12 Jun '12

Hi, can you tell me how the energy value olde in the example script http://salilab.org/modeller/manual/node264.html (olde, dstate) = self.energy(state) is calculated? For an restraints file with N (physical.bond, physical.ca_distance, ...) entries in it, how does the formula look like: sum_i^N log(rsr_i), where rsr_i is defined as in http://salilab.org/modeller/manual/node469.html? Are there any scaling factors? Best regards Armin

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Heterodimer modeling
by Xiongzhuo Gao 11 Jun '12

11 Jun '12

Dear Modellers, I'm building a heterodimer with a homodimer template. I have the template pdb file (dimer.pdb) and the sequence file of the heterodimer (hetero.ali). Here is the hetero.ali file: >P1;hetero sequence:to_model:1:A:859:B:853::: AAAAAAAAAAAAAAAAAAAAA/BBBBBBBBBBBBBBBBB There are 859 a.a. in one chain and 853 a.a. in the other chain. I didn't type the exact number of a.a. here. The following is the script I used for alignment: from modeller import * env = environ() aln = alignment(env) mdl = model(env, file='dimer', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='dimerAB', atom_files='dimer.pdb') # I used "dimerAB" to point out both chain A and chain B for alignment. I don't know whether it is correct. aln.append(file='hetero.ali', align_codes='hetero') aln.align2d() aln.write(file='hetero-dimerAB.ali', alignment_format='PIR') aln.write(file='hetero-dimerAB.pap', alignment_format='PAP') The script running result showed the two chain of the heterodimer aligned to one chain of the template. Would you kindly tell me how I can get the correct alignment? Thank you. Xiongzhuo Gao BMCB Department University of New Hampshier Durham, New Hampshire 03824

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Chimeric protein - residue numbers
by Larsson, Per (pl6n) 05 Jun '12

05 Jun '12

Hi! I am trying to build a model using the automodel class, based on two known structures where I want parts of the model to be based on structure A and parts on structure B. My alignment file looks like this: >P1;protein_a structureX:protein_a:1::238::::: aaaaaaaaaa---------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa------------------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa--------------------------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-----------------------aaaaaaaaaaaaaaaa---------* >P1;protein_b structureX:protein_b:1::93::::: ----------bbbbbbbbb-----------------------------------bbbbbbbbbbbbbbbbbb-------------------------------------------bbbbbbbbbbbbbbbbbbbbbbbbbb-------------------------------------------------bbbbbbbbbbbbbbbbbbbbbbb----------------bbbbbbbb* >P1;chimera sequence:chimera:1::238::::: aaaaaaaaabbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaabbbbbbb* In my structure files, protein_a contains residues from 1-238. The residues in protein_b are a subset of the residues in protein_a, but I want restraints to be derived from protein_b for some parts of the final model. When running this in Modeller (v 9.10) i get the error read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 11) which I believe comes from the fact that since protein_a contains all residues, Modeller does not skip residues in the protein_a file, and a mismatch occurs. Do I need to remove residues from the structure in protein_a, or is there some way to tell Modeller to skip those residues when matching the sequence of residues in the structure file with the sequence of residues in the alignment file? Or alternatively tell Modeller to use restraints from only protein_b for parts of the model? Thanks /Per Larsson

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Chimeric alignment - residue numbers
by Larsson, Per (pl6n) 05 Jun '12

05 Jun '12

Hi! I am trying to build a model using the automodel class, based on two known structures where I want parts of the model to be based on structure A and parts on structure B. My alignment file looks like this: >P1;protein_a structureX:protein_a:1::238::::: aaaaaaaaaa---------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa------------------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa--------------------------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-----------------------aaaaaaaaaaaaaaaa---------* >P1;protein_b structureX:protein_b:1::93::::: ----------bbbbbbbbb-----------------------------------bbbbbbbbbbbbbbbbbb-------------------------------------------bbbbbbbbbbbbbbbbbbbbbbbbbb-------------------------------------------------bbbbbbbbbbbbbbbbbbbbbbb----------------bbbbbbbb* >P1;chimera sequence:chimera:1::238::::: aaaaaaaaabbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbaaaaaaaaaaaaaaaabbbbbbb* In my structure files, protein_a contains residues from 1-238. The residues in protein_b are a subset of the residues in protein_a, but I want restraints to be derived from protein_b for some parts of the final model. When running this in Modeller (v 9.10) i get the error read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 11) which I believe comes from the fact that since protein_a contains all residues, Modeller does not skip residues in the protein_a file, and a mismatch occurs. Do I need to remove residues from the structure in protein_a, or is there some way to tell Modeller to skip those residues when matching the sequence of residues in the structure file with the sequence of residues in the alignment file? Or alternatively tell Modeller to use restraints from only protein_b for parts of the model? Thanks /Per Larsosn

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Invitation to connect on LinkedIn
by Arvind Pal via LinkedIn 04 Jun '12

04 Jun '12

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signal peptide structure modeling
by Kwee Hong 31 May '12

31 May '12

Hi, I would like to model signal peptide structure. I would like to know is this possible with MODELLER? Or is there any relevant modeling server? Thanks, Joyce

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Re: [modeller_usage] PD: Re: optimization schedule
by M 31 May '12

31 May '12

Thank you very much, that was exacly what I wanted to know. Sorry for my poor description of those problems. > On 5/31/12 11:06 AM, M wrote: > > Thank you very much. One last question: how are the atoms (residues) > > chosen for individual CG step? For example if residue span range is > > 10, does it mean that only first residues are optimized? > > I don't know what you mean by "first residues" here. The schedule isn't > for picking which atoms are optimized (that is the job of the selection > - see automodel's select_atoms method - which by default is all atoms). > The schedule picks which *restraints* are optimized. If the span range > is 10, that means all atom-atom restraints that act on atoms in residues > at most 10 apart in sequence are optimized. > > 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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Re: [modeller_usage] PD: Re: optimization schedule
by M 31 May '12

31 May '12

Thank you very much. One last question: how are the atoms (residues) chosen for individual CG step? For example if residue span range is 10, does it mean that only first residues are optimized? > On 5/31/12 10:26 AM, M wrote: > > I was asking about the Conjugate gradients optimization > > initializations (each step of adding additional restraints), not > > about the steps of one CG process. > > Before the schedule is used in comparative modeling, schedule steps with > a range larger than the length of your sequence are removed, since they > are redundant; see > http://salilab.org/modeller/9.10/manual/node267.html > > 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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