June 2012 - modeller_usage

A question about using multiple template
by Xiongzhuo Gao 25 Jul '12

25 Jul '12

Dear Modellers, Our lab is studying the structure of the rod and cone photoreceptor phosphodiesterase that is central to the visual signaling pathway. The rod enzyme contains a regulatory tandem GAF domain (GAFa-GAFb) and a catalytic domain, and exists as a heterodimer (PDE6A and PDE6B). There are currently no full length crystal structures for this catalytic heterodimer, only a structure for the GAFa regulatory domain of cone PDE6C, the GAF domain that binds cGMP noncatalytically. The most homologous protein to PDE6 is the PDE that is abundant in vascular smooth muscle and is the target for Viagra, PDE5 (a catalytic homodimer). There is a dimeric structure for the PDE5 tandem GAF domains (GAFa-GAFb) and for the isolated, monomeric catalytic domain, but no full-length structures. cGMP binds to the GAFa domain of PDE5, the same as PDE6. A more distantly related PDE, PDE2, has a crystal structure of the nearly full-length, dimeric protein, but unfortunately the GAF domains of PDE2 occur in an opposite order compared to PDE5 and PDE6 (i.e., the cGMP binding site is in GAFb). See the attached diagram for a visual description of the domain organization of the three PDEs. We are trying to build a homology model for PDE6 heterodimer. The homology model when PDE6 is threaded onto the PDE2 structure is poor. In contrast, structural homology modeling of PDE6 GAF and catalytic domains using PDE5 as a template gives excellent results. Unfortunately, it is only in the PDE2 structure that the molecular architecture of the nearly full-length dimer has been determined, namely the region between the GAF and catalytic domains and the relationship of the two catalytic domains. Is there some way to rearrange (cut-and-past) the individual domains in the sequence alignment to allow PDE5 to serve for the template for those domains that have been determined, while still using the PDE2 template to thread the PDE6 linker region and to define the relationship of the two catalytic domains with each other? Could you kindly give us some advice on how to do the alignment and build the model? I would greatly appreciate your help. Best, Xiongzhuo Gao Molecular, Cellular and Biomedical Sciences Department University of New Hampshire Durham, New Hampshire 03824 Phone: 603-862-3829

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HETATM MSE records
by Thomas Gaillard 29 Jun '12

29 Jun '12

Hi, I have noticed that some HETATM records are read by Modeller and automatically handled as corresponding standard residues (for example MSE -> MET), even if env.io.hetatm is set to False. It is explained at http://salilab.org/modeller/9.9/manual/node171.html. I would like to know if you could suggest a way to disable this behaviour and really ignore all HETATM records. I have tried to remove the MSE line from restyp.lib and provide my reduced restyp.lib with env = environ(restyp_lib_file='myrestyp.lib'), but this does not seem to work as the MSE still appears to be read and taken into account as MET by Modeller. Thanks for your time, -- Thomas Gaillard Maître de conférences Laboratoire de Biochimie Ecole Polytechnique 91128 Palaiseau cedex tel: +33 1 69 33 48 62 fax: +33 1 69 33 49 09 thomas.gaillard(a)polytechnique.edu http://bioc.polytechnique.fr/~gaillard

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Sequence Mismatch Errors
by Austin Baker 25 Jun '12

25 Jun '12

All, I am trying to run a 2d alignment and keep getting a number of errors that I have been unable to rectify. In addition to the error message presented below I've also been getting one that says "Alignment sequence not found in the pdb file". Much appreciated in advance Austin ERROR MESSAGE: Traceback (most recent call last): File "align2d_HDAC9a_Cat.py", line 21, in <module> align_block=aln_block) File "/Library/modeller-9.10/modlib/modeller/alignment.py", line 299, in align2d smooth_prof_weight, weights_type) _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : ALIGNMENT FILE: >P1;HDAC9a_Cat sequence:HDAC9a_Cat:1:A:251:A::::: PGSATGIAYDPLMLKHQCVCGNSTTHPEHAGRIQSIWSRLQETGLLNKCERIQGRKASLEEIQLV HSEHHSLLYGTNPLDGQKLDPRILLGDDSQKFFSSLPCGGLGVDSDTIWNELHSSGAARMAVGCVIELAS KVASGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYA DPSILYISLHRYDEGNFFPGSGAPNEVRFISLEPHFYLYLSGNCIA* >P1;2vqj StructureX:2vqj.pdb:6:A:236:A:::0.00: 0.00 GAMTKPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTV HSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFK VATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSD PSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAP DVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLG NELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAETVT* SCRIPTS # 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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missing residue build using automodel
by Mary Varughese 23 Jun '12

23 Jun '12

Hi, This is the align_multiple.ali file of automodel example, C; A multiple alignment in the PIR format; used in tutorial >P1;5fd1 structureX:5fd1:1 :A:106 :A:ferredoxin:Azotobacter vinelandii: 1.90: 0.19 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA EVWPNITEKKDPLPDAEDWDGVKGKLQHLER* >P1;1bqx structureN:1bqx: 1 :A: 77 :A:ferredoxin:Bacillus schlegelii:-1.00:-1.00 AYVITEPCIGTKCASCVEVCPVDCIHEGEDQYYIDPDVCIDCGACEAVCPVSAIYHEDFVPEEWKSYIQKNRDFF KK-----------------------------* >P1;1fdx sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00 AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED----------------- -------------------------------* modelmultilple.py has this code; a = automodel(env, alnfile = 'align-multiple.ali', # alignment filename knowns = ('5fd1', '1bqx'), # codes of the templates sequence = '1fdx') # code of the target I dont understand this. I mean the real purpose of this code. I thought 'sequence' is the target we want to achieve and it has no gaps. but here 1fdx has so many breaks. Could anyone tell me the real meaning of this alignment. Thanking you -- Mary Varughese Research Scholar School of Pure and Applied Physics Mahatma Gandhi University India

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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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