- modeller_usage - salilab.org

modelling a protein withtow chains
by Houcemeddine Othman 04 Apr '11

04 Apr '11

Hi I try to model an heterodimer using this alignment >P1;1DZB2 structureX:1DZB2:1:A:107:B:::: QVKLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCAR-----WDWYFDVWGQGTTVTVSSG/ ------------DIELTQSPSSMYTSLGERVTITCKASQDINSYLRWFQQKPGKSPKTLIYYATSLADGVPSRFSGSGSGQDYSLTISSLESDDTTTYYCLQHGESPYTFGGGTKLEIK---------* >P1;atc sequence::::::::: -VKLQQSGGGLVQPGGSLKLSCAASGFDFSRYWMSWVRQAPGKGLEWIGEINPDSSTINYTPSLKDTFIISRDNAKNTLYLQMSKVRSEDTALYYCARQGYDGYHWYFDVWGQGTTVTVSSE/ SLDLGGGGGGGGDIQLTQSPSSLSASVGETVTLTCGASENIYGGLNWYQRKQGKSPQLLIYGATKLADGMSSRFSGGGSGRQYFLKITSLHPDDVATYYCQNVLSNPLTFGAGTKLELKRADAAPTVS* each time it gives me this error message define__595E> Number of selected atoms in sets 2 & 3 is not the same: 121 128 Can you tell me please what's wrong in my alignment file script used: # Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = environ() # directories for input atom files env.io.atom_files_directory = './' a = MyModel(env, alnfile = 'ali.pir', knowns = '1DZB2', sequence = 'atc') a.starting_model= 1 a.ending_model = 1 a.make()

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Modeller 9.9 release
by Modeller Caretaker 04 Apr '11

04 Apr '11

The new version of Modeller, 9.9, 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 9.9 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.9 is primarily a bugfix release relative to the last public release (9v8). Major user-visible changes include: # The Windows version of Modeller is now only supported on XP Service Pack 2 or later. If you want to run Modeller on Windows 98, ME, 2000, or NT, use Modeller 9v8. # Added support for Python 2.7 to Windows and Linux Modeller; Python 2.5 is now supported on all platforms. # Initial models generated by automodel now always contain valid PDB coordinates, i.e. each coordinate is in the range -999.999 to 9999.999. # During loop modeling, if atoms are missing from the initial model, loopmodel.loop.write_defined_only can be set True to write out PDBs containing only non-loop atoms present in the initial model. # When reading new-style PDB files (with element names in columns 77-78) Modeller will now use this information to determine whether an atom is a hydrogen. (With old-style or non-conformant PDB files, it will continue to guess based on the atom name, so will not read mercury ions for example unless env.io.hydrogen=True, since it cannot unambiguously determine whether HG is mercury or "hydrogen bonded to CG".) See the Modeller manual for a full change log: http://salilab.org/modeller/9.9/manual/node38.html If you encounter bugs in Modeller 9.9, please see http://salilab.org/modeller/9.9/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 you 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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salign: specify chains to superpose
by Yingjie Lin 01 Apr '11

01 Apr '11

Hi Modellers, I wonder what is the best way to superpose two multi-chain proteins, and explicitly specify the chains to include in superposition. I know that I can read only the wanted chains into the alignment, but I also want to make sure that the other chains move according to the superposition. Here are two ways we could think of: 1. read only the wanted chains and do superposition. Then move the other chains accordingly using functions like selection.rotate_origin(), selection.rotate_mass_center() and selection.transform(). 2. model1 <= all chains in protein A model2 <= all chains in protein B model3 <= the chain(s) selected for superposition in protein B first, superpose model3 to model1 (model3 is moved) second, superpose model2 to model3 (model2 is moved) Are there any better ways? Thank you. Yingjie

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Are gap in target and template same.
by Ashish Runthala 01 Apr '11

01 Apr '11

Dear Modellers, I am facing an interesting problem. Are gaps in target and template same, as shown below. Target AAAAA AA--A AA--A Template AA--A AAAAA AA--A CaseI CaseII CaseIII Are these three cases I,II, & III modelled the same way. How will the gap penalties be incorporated in these three cases, when the modeller calculates the alignment score. PLEASE PROVIDE ME COMPLETE DETAILS ABOUT GAP PENALTIES IN THESE THREE CASES. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 59
by Ashish Runthala 01 Apr '11

01 Apr '11

Dear Lin, I wrote a script in C to do all that. You can use it to do the analysis for specific chains. You can even do the analysis for specific segment of residues in a specific chain. If you want, I will provide you the help by providing the binary. 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: Friday, April 1, 2011 10:01:26 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 59 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. unsubscribing (Bo Yang) 2. salign: specify chains to superpose (Yingjie Lin) 3. salign: specify chains to superpose (Yingjie Lin) 4. Are gap in target and template same. (Ashish Runthala) ---------------------------------------------------------------------- Message: 1 Date: Thu, 31 Mar 2011 08:07:11 -0700 (PDT) From: Bo Yang <n62star(a)yahoo.com> Subject: [modeller_usage] unsubscribing To: modeller_usage(a)salilab.org Message-ID: <676504.10553.qm(a)web36906.mail.mud.yahoo.com> Content-Type: text/plain; charset="us-ascii" unsubscribing

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salign: specify chains to superpose
by Yingjie Lin 31 Mar '11

31 Mar '11

Hi Modellers, I wonder what is the best way to superpose two multi-chain proteins, and explicitly specify the chains to include in superposition. I know that I can read only the wanted chains into the alignment, but I also want to make sure that the other chains move according to the superposition. Here are two ways we could think of: 1. read only the wanted chains and do superposition. Then move the other chains accordingly using functions like selection.rotate_origin(), selection.rotate_mass_center() and selection.transform(). 2. model1 <= all chains in protein A model2 <= all chains in protein B model3 <= the chain(s) selected for superposition in protein B first, superpose model3 to model1 (model3 is moved) second, superpose model2 to model3 (model2 is moved) Are there any better ways? Thank you. Yingjie

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unsubscribing
by Bo Yang 31 Mar '11

31 Mar '11

unsubscribing

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 57
by Ashish Runthala 29 Mar '11

29 Mar '11

Thomas, I don't expect all this what you replied. See i understand all that what you told. But there is a big problem there, to try multiple alignments and iterated trials to land on good models(which itself is ambiguous, as you can't really discriminate good and bad model, until you have answer or GDT). So i am developing a complete in-house algorithm to result in the best representative alignment from the considered templates against the target. So i want to incorporate secondary structure information or localized fold topologies to generate a 3D alignment file. Hence i am looking forward for a python script which can be integrated with MODELLER to result in the information like this. Template1> HCLCH Template2> HCLHH Target> xxxxx (H=Helix. C=Coil, L=Loop) I JUST NEED SECONDARY STRUCTURE INFORMATION OF EACH ALIGNED RESIDUE OF EACH TEMPLATE, BASED ON ITS PROBABILITY TO LAND IN SAME FOLD, AS PER THE AVAILABLE PROXIMAL RESIDUES. Ya, and by the way, SCRWL won't help if you choose bad template/alignment. Refinement improves GDT_TS scores by just 4 or 5%. Good coordinate selection is most important. MODELLER also can't result in good models, if you mix up incorrect template informations, and the problem becomes more complex, when the new fold comes up. Thanks for support. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "Thomas Evangelidis" <tevang3(a)gmail.com> To: "Ashish Runthala" <ashishr(a)bits-pilani.ac.in> Cc: "modeller usage" <modeller_usage(a)salilab.org> Sent: Tuesday, March 29, 2011 4:46:20 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment file On 27 March 2011 10:05, Ashish Runthala < ashishr(a)bits-pilani.ac.in > wrote: Dear Thomas, I will write it clearly this time. Take simplest case.Suppose, I have a structural/sequence alignment of 3 templates against a target sequence. Now, as modeller predicts tertiary conformation for the target sequence, it surely predicts the alignment based secondary structure information against all the templates. So now i want that specific secondary structure information along with the alignment file for the aligned templates against the target sequence. Now my C script will take on this alignment file to generate the representative best possible optimum alignment for the considered target sequence. These models in my tried iterations for the CASP8 targets gave excellent results. So if I understand correctly, your script creates alternative alignments, then runs Modeller to build a model of the target from each alignment, it reads the secondary structure (SS) from each model, and based on this SS it judges which alternative alignment is the optimum. Is this how it works? Can you elaborate on the algorithm? What are the criteria to select the optimum alignment and what is the answer you seek from the mailing list? I think i made myself clear this time. By the way, what you are working on. I think you are also working on the same topics. What you have redefined? I am interested to know that. I've been working on optimization at the alignment level in the past, but in my approach the selection of the optimum alignment and template combination is based on the overall native-likeness of the resulting homology models, not just the secondary structure of the target. More specifically, I create homology models at several levels of optimization and refinement from alternative alignments and different template combinations. The resulting models are sorted according to the DOPE-HR score, and the best of them undergo side-chain optimization with SCWRL4, and extensive stereochemical tests with the programs PROCHECK and WHAT_CHECK to select the best of them. The whole procedure is streamlined and parallelized with a combination of bash and python scripts. However, it has been tested only on my cases and a few CASP9 targets. More details can be found at: https://sites.google.com/site/hmopalpipeline/home (I will update the website tomorrow) Thanks in advance, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "Thomas Evangelidis" < tevang3(a)gmail.com > To: "Ashish Runthala" < ashishr(a)bits-pilani.ac.in > Cc: "modeller usage" < modeller_usage(a)salilab.org > Sent: Saturday, March 26, 2011 6:06:02 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment file On 26 March 2011 07:47, Ashish Runthala < ashishr(a)bits-pilani.ac.in > wrote: Dear Thomas, You mentioned the free tools in details. I appreciate that. But what i don't understand is to manually call everyone, and then keep on doing it, is tedious but fun it is. So if I get it right this time, you didn't ask what commercial free tools are available to display your sequence alignment along with the secondary structure, is that correct? Could you please be more careful with your syntax cause it's kind of difficult to follow you. I had a query that template secondary structure information is there in templates, but with indels, that may be disturbed. I mean the native information is deteriorated. So if based on indels, available in current alignment, if i can link directly to a python script. So that my next programme to generate the optimal alignment will become successful, as i did all of these several times manually, to design the algorithm to generate best representative alignment. So you want to write a python script that can cope with indels inside SSEs. Namely, given a structure-based alignment between your target and templates, you want to select which of the following alignments is the optimum: target > HCSIHHSC Template1> HCSIHISC Template2> HCSHHISC ------------------------------------------------------- target > HCS-IHHSC Template1> HCS-IHISC Template2> HCSH-HISC ------------------------------------------------------- target > HCSI-HHSC Template1> HCS-IHISC Template2> HCS-HHISC etc. Is this what you seek? Will you please elaborate this time. Thanks, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "Thomas Evangelidis" < tevang3(a)gmail.com > To: "Ashish Runthala" < ashishr(a)bits-pilani.ac.in > Cc: "modeller" < modeller_usage(a)salilab.org > Sent: Friday, March 25, 2011 4:50:42 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment file Maestro from Schrodinger can display both the predicted secondary structure elements (SSE) of the target and the SSE of the templates above the alignment dynamically (namely if you change the alignment the SSEs are changed accordingly). Alternatively you can use the following commercial free tools: ESPript ( http://espript.ibcp.fr/ESPript/ESPript/ ): can create an image of your alignment with the SSEs of your templates above it. No SSE of the target is displayed though. MolIDE ( http://dunbrack.fccc.edu/molide/index.php ): I have the notion that this alignment editor (and not only) can display both the predicted SSE of the target and the SSE of the templates. However, I didn't manage to run it yet due to compilation problems. I intend to give it a try in the near future. STRAP ( http://3d-alignment.eu/ ): it can do both but the GUI is not handy in Linux (windows and fonts are unequal, etc.). Finally you can add a row with the secondary structure (as you wrote it in your email) above each sequence in your alignment editor. I prefer Jalview and like to play around with groups and colors. See the attached image for an example. SSE of your templates can be retrieved from PDB (e.g. http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2IXF&chainId=A ) whereas the SSE of your target can be predicted by Jpred3 ( http://www.compbio.dundee.ac.uk/www-jpred/ ). HTH, Thomas On 25 March 2011 05:47, Ashish Runthala < ashishr(a)bits-pilani.ac.in > wrote: Dear Modellers, Suppose i have two templates, and a target sequence. Instead of sequence alignment based file, i want to consider the secondary structure information, like given below Template1> HCSIHISC Template2> HCSHHISC H=Helix, C=Coil, S-Strand, I=Indels Is it possible to get the alignment in this case for multiple templates against the target sequence( whose structure can also be represented as best aligned folds) Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Secondary structure restraints
by Lilit Nersisyan 28 Mar '11

28 Mar '11

Hi, I try to refine a long loop in my protein model by adding several secondary structure restraints and I've confronted the following problem: some restraints do not have any effect unless other ones are removed from the restraint list. In other words, after removing some of the restraints others start working properly. I would like to know the reasons and how can this problem be solved. I use the following script: from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = [’.’, ’../atom_files’] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: # rsr.append(file=’my_rsrs1.rsr’) # Residues 20 through 30 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range(’20:’, ’30:’))) # Two beta-strands: rsr.add(secondary_structure.strand(self.residue_range(’1:’, ’6:’))) rsr.add(secondary_structure.strand(self.residue_range(’9:’, ’14:’))) a = MyModel(env, alnfile = ’alignment.ali’, knowns = ’5fd1’, sequence = ’1fdx’) a.starting_model= 1 a.ending_model = 1 a.make() Thank you for attention. -- Lilit Nersisyan Institute of Molecular Biology NAS RA E-mail: txgt.lilit.nersisyan(a)gmail.com Tel.: +37494 601703

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Sidechains Refinement and Symmetry definition
by Giampaolo 28 Mar '11

28 Mar '11

Dear Modeller Caretaker, I'm studying an homotetramer and i want to identify new sidechain orientations on a specific helix segment without any more changes in the protein structure of my initial pdb. So i tried the loopmodel routine: ################################################################### from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() env.io.atom_files_directory = ['.'] class MyLoop(loopmodel): def select_loop_atoms(self): return selection(self.residue_range('232:A', '268:A'), self.residue_range('232:B', '268:B'), self.residue_range('232:C', '268:C'), self.residue_range('232:D','268:D')).only_sidechain() m = MyLoop(env, inimodel = 'herg_merged.pdb', # initial model sequence = 'herg_trg') # target m.loop.starting_model= 1 # index of the first model m.loop.ending_model = 50 # index of the last model m.loop.md_level = refine.very_fast m.make() # do refinement ########################################################### Therefore, I obtained 50 models with different sidechain-orientations over the specified segments. My question is the following: ?- Is it possible to preserve the symmetry of the sidechains over all the subunits? or...to perform a total symmetry of the models by a post-processing step of refinement? Furthermore, I tried also to define special symmetry restraints, but all the 50 models resulted equals between them... it seems that nothing happens: ############################################ def special_restraints(self, aln): s1 = selection(self.chains['A']) s2 = selection(self.chains['B']) s3 = selection(self.chains['C']) s4 = selection(self.chains['D']) self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) self.restraints.symmetry.append(symmetry(s1, s3, 1.0)) self.restraints.symmetry.append(symmetry(s1, s4, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) ################################################# Thank's in advance for your time and consideration My regards, Giampaolo

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