- modeller_usage - salilab.org

Simple modeling with ligand
by Francesco Pietra 30 Jul '08

30 Jul '08

I was trying to widen the script model-single.log of tutorial "Basic example' to treat also a ligand from modeller import * from modeller.automodel import * env = environ() env.io.hetatm = True a = automodel(env, alnfile='xxx.ali', knowns='XXX', sequence='yyy', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() The five model were built without the ligand. Much obliged for getting a correction of this script. Thanks francesco pietra

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Appending model pdb files
by Francesco Pietra 29 Jul '08

29 Jul '08

As I want to append to one another model pdb files (for chains A, B, C, etc) to build a multimer, may I ask about what I was unable to trace: (1) What does "1SG" at columns 74-76 (PDB numbering) mean? (2) Why serial numbers (Atom number + 1) are reported at column 80 (PDB numbering)? (3) Should serial numbers said at (2) above be updated (like the Atom number at column 11) when concatenating the model pdb files? (4) Why the Chain identifier is not printed in model pdb files (which is obviously needed for concatenation), or there was a way to specify it be printed? (5) When programming Python I take for obvious that it starts reading the columns from zero, not 1. OK? Thanks francesco pietra

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Editing pdb file for a multimer
by Francesco Pietra 29 Jul '08

29 Jul '08

I plan to model a homomultimer by modeling separately each chain and then combining the results. To this concern, are python scripts available for (a) inserting the chain label at position 22 (which was not inserted the way I did), (b) renumbering the atom serial number, TER inclusive? I understand I have to learn seriously how to program with python. Thanks francesco pietra

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working & accuracy of modeller
by rsachdeva＠imtech.res.in 28 Jul '08

28 Jul '08

Dear all, I have some basic queries regarding modeller working & its performance. 1) What is the accuracy of model building by modeller? 2) I have read in the modeller mailing list that in the case of multiple templates, modeller uses weighted sum over all the templates. Does this mean that spatial restraints are derived individually from the alignment between first template & query sequence and from the alignment between the second template & the query sequence? Then these resraints are added and weights are applied to that template according to the local similarity with the query sequence? Anyone please correct me if I am wrong? 3) I have built a model using 2 templates with modeller9v2. RMSD (only backbone atoms) between the model & the first template is 1.6 ang & with second is 3.3. Sequence identity is higher between the target sequence & first template as compared to that of the second template. How can I calculate the accuracy of this model in terms of percentage? What is the way of calculating the accuracy of model building? Looking forward to your reply? Kindly reply and enhance my knowledge. Thanks in advance Ruchi

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Mismatch alignment-pdb
by Francesco Pietra 24 Jul '08

24 Jul '08

I must have posted the same message to a wrong modeller list. Sorry. I fear to be unable to read published alignments, though both alignments and pdb file are from the same publication. What I did is to build the ali file by copy/pasting the whole sequence alignment. Perhaps a shortcut that is not allowed. The first line copy/pasted for "structure" reads: ---------------------------------------------MMDLKVDEE---------EVDSGQPVSIQAFASSSTLHGISHIFSYE---------R the last G being 30. The corresponding line for "sequence" reads: ----------------------------------------------MELKAEEE---------EVGGVQPVSIQAFASSSTLHGLAHIFSYE---------R again, the last G being 30. These lines (and all following ones in a continuous sequence) were copy/pasted to create the two PIR files for ali. >From the pdb corresponding to "structure" the list of residues begins with L(42), K(43), A(44), V(45) for chain A, so that I set 42 as the starting residue, chain A. I expected a mismatch. In fact the log file reads; read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 1) Alignment MMDLKVDEEEVDSGQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLA PDB LKRVVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLN Match * * * * Alignment residue type 11 (M, MET) does not match pdb residue type 10 (L, LEU), for align code XXXX (atom file XXXX), pdb residue number "42", chain "A" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 XXXX Thanks for help about this extremely naive doing. francesco pietra

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another doutbs about file
by Amanda Moraes 24 Jul '08

24 Jul '08

Thank you very much! I have another question: the sequences in PIR file .. do they all have to have the same size? I´m asking because my templates have different sizes and align in different places... what should I do? Even if I tell modeller where to start and to end, the sequences selected are not the same size... is that a problem? Thank you in advance, Amanda amaia Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses

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doutbs about file
by Amanda Moraes 22 Jul '08

22 Jul '08

Hello! My name is Amanda Maia and I´m a beginner using Modeller. I´m having some trouble finding the answers to my questions on the manual. Could you help me? I have a sequence that aligns (BLAST pdb)with various structures on PDB within an average identity of 35%. Since I need to use as much models as I can get, I´m writing a PIR file with 5 templates. But one (1MDY) has 2 chains (out of 4) that blast quotes (B and E). Do I have to make a PIR line to each one? And a pdb file for each one too? Example: >P1;molde1MDYB structureX:molde1MDYB:FIRST:@:LAST :@:myoD:myoD: 2.00:-1.00 ----------------------------------------------------------------------------------------------------------------------------TTNADRRKAATMR--ERRR------LSKVNEAFETLKRSTSSNPN-----------QRLPKVEILR--------NAIRYIEGLQAL-LRD-------------------------------------* >P1;molde1MDYA structureX:molde1MDYA:FIRST:@:LAST :@:myoD:myoD: 2.00:-1.00 ----------------------------------------------------------------------------------------------------------------------MELKRKTTNADRRKAATMR--ERRR------LSKVNEAFETLKRSTSSNPN-----------QRLPKVEILR--------NAIRYIEGLQAL-LRD-------------------------------------* Thank you in advance! Amanda Maia Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses

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Fwd: The results of your email commands
by 刘君 22 Jul '08

22 Jul '08

I don't understand. Done. ---------- Forwarded message ---------- From: <modeller_usage-bounces(a)salilab.org> Date: 2008/7/22 Subject: The results of your email commands To: snailliujun(a)gmail.com The results of your email command are provided below. Attached is your original message. - Unprocessed: byBteSBwZXJzb25hbAplbWFpbC4gSSBhcHByZWNpYXRlIHlvdXIgZmVlZGJhY2sgYXMgc29vbiBh cyBwb3NzaWJsZS4gT3Igd291bGQgeW91CnBsZWFzZSBjaGVjayB5b3VyIHN5c3RlbSBrZXJuZWwg b2YgeW91ciBzZXJ2ZXIsIG9yIHBlcmhhcHMgaXQncyBqdXN0IGEKcGVyc29uYWxseSBvcGVyYXRp bmcgbWlzdGFrZT8KCnNpbmNlcmVseSB5b3VycywKc25haWxsaXVqdW4KCgotLS0tLS0tLS0tIEZv cndhcmRlZCBtZXNzYWdlIC0tLS0tLS0tLS0KRnJvbTogTW9kZWxsZXIgQ2FyZXRha2VyIDxtb2Rl bGxlci1jYXJlQHNhbGlsYWIub3JnPgpEYXRlOiAyMDA4LzcvMTgKU3ViamVjdDogUmU6IFttb2Rl bGxlcl91c2FnZV0gYSBxdWVzdGlvbiBvbiBNT0RFTExFUiB1c2FnZQpUbzogSXZhbiBBbmlzaGNo ZW5rbyA8YW5pc2hjaGVua28uaXZhbkBnbWFpbC5jb20+CrOty82juiBtb2RlbGxlcl91c2FnZUBz YWxpbGFiLm9yZwoKCkl2YW4gQW5pc2hjaGVua28gd3JvdGU6Cj4gSSBkZWFsIHdpdGggYSBwZXB0 aWRlICgzNSByZXNpZHVlcyBsb25nKS4gSSBrbm93IGl0cyBhbWlubyBhY2lkIHNlcXVlbmNlCj4g YW5kIGEgc2V0IG9mIG1lYW4gdmFsdWVzIGZvciBwaGktIGFuZCBwc2ktIGRpaGVkcmFscyBhbmQg dGhlIHJlc3BlY3RpdmUKPiBjb25maWRlbmNlIGludGVydmFsIGZvciBlYWNoIGRpaGVkcmFsIGFu Z2xlLiBUaGUgZGF0YSBpcyBvYnRhaW5lZCBmcm9tCj4gdGhlIE5NUiBleHBlcmltZW50cy4gVGhl IGFpbSBpcyB0byBvYnRhaW4gYSBzdHJ1Y3R1cmUgd2l0aCB0aGUKPiBtYWluLWNoYWluIGRpaGVk cmFscyBseWluZyB3aXRoaW4gdGhlIGNvcnJlc3BvbmRpbmcgY29uZmlkZW5jZSBpbnRlcnZhbAo+ IGZvciBldmVyeSByZXNpZHVlLiBTaWRlIGNoYWlucyBjYW4gdGFrZSBhbnkgY29uZm9ybWF0aW9u LiBIb3cgY2FuIHN1Y2gKPiByZXN0cmFpbnRzIGJlIGRlc2NyaWJlZCBpbiBNT0RFTExFUj8KCjEu IFJlYWQgaW4gdGhlIGluaXRpYWwgc3RydWN0dXJlIChzZWUgdGhlIG1hbnVhbCBmb3IgY29tcGxl dGVfcGRiKSBvcgpidWlsZCBhbiBleHRlbmRlZCBjaGFpbiBmcm9tIHRoZSBBQSBzZXF1ZW5jZSAo bW9kZWwuYnVpbGRfc2VxdWVuY2UpLgoKMi4gQWRkIHJlc3RyYWludHMgb24gZWFjaCBkaWhlZHJh bC4gU2VlIFJlc3RyYWludHMuYWRkLiBUbyBnZXQgdGhlIGxpc3QKb2YgYXRvbXMgZm9yIGVhY2gg ZGloZWRyYWwgdHlwZSBpbiBlYWNoIHJlc2lkdWUsIHNlZSBSZXNpZHVlLnBoaSBhbmQKRGloZWRy YWwuYXRvbXMuIEZvciBleGFtcGxlLCB0byBjb25zdHJhaW4gZXZlcnkgcGhpIGFuZ2xlIGluIHRo ZSBtb2RlbAonbScgdG8gMCArLy0gMC4xIHJhZGlhbnMsIHVzaW5nIGEgR2F1c3NpYW4gcmVzdHJh - Ignored: aW50OgoKZm9yIHJlcyBpbiBtLnJlc2lkdWVzOgogICAgaWYgcmVzLnBoaSBpcyBub3QgTm9uZToK ICAgICAgICBhdG9tcyA9IHJlcy5waGkuYXRvbXMKICAgICAgICBmID0gZm9ybXMuZ2F1c3NpYW4o Z3JvdXA9cGh5c2ljYWwuZGloZWRyYWwsCiAgICAgICAgICAgICAgICAgICAgICAgICAgIGZlYXR1 cmU9ZmVhdHVyZXMuZGloZWRyYWwoKmF0b21zKSwKICAgICAgICAgICAgICAgICAgICAgICAgICAg bWVhbj0wLCBzdGRldj0wLjEpCiAgICAgICAgbS5yZXN0cmFpbnRzLmFkZChmKQoKMy4gWW91IG1h eSBhbHNvIHdhbnQgdG8gYnVpbGQgb3RoZXIgc2V0cyBvZiByZXN0cmFpbnRzLCBmb3IgZXhhbXBs ZQpzdGVyZW9jaGVtaWNhbCByZXN0cmFpbnRzLiBTZWUgUmVzdHJhaW50cy5tYWtlLgoKNC4gT3B0 aW1pemUgdGhlIHN0cnVjdHVyZS4gU2VlIGNvbmp1Z2F0ZV9ncmFkaWVudHMoKS4KCiAgICAgICBC ZW4gV2ViYiwgTW9kZWxsZXIgQ2FyZXRha2VyCi0tCm1vZGVsbGVyLWNhcmVAc2FsaWxhYi5vcmcg ICAgICAgICAgICAgaHR0cDovL3d3dy5zYWxpbGFiLm9yZy9tb2RlbGxlci8KTW9kZWxsZXIgbWFp bCBsaXN0OiBodHRwOi8vc2FsaWxhYi5vcmcvbWFpbG1hbi9saXN0aW5mby9tb2RlbGxlcl91c2Fn ZQpfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fXwptb2RlbGxl cl91c2FnZSBtYWlsaW5nIGxpc3QKbW9kZWxsZXJfdXNhZ2VAc2FsaWxhYi5vcmcKaHR0cHM6Ly9z YWxpbGFiLm9yZy9tYWlsbWFuL2xpc3RpbmZvL21vZGVsbGVyX3VzYWdlCgoKCi0tIApUb21vcnJv dyBpcyBhbm90aGVyIGRheS4K - Done. ---------- 已转发邮件 ---------- From: "刘君" <snailliujun(a)gmail.com> To: modeller_usage-request(a)salilab.org Date: Tue, 22 Jul 2008 23:55:40 +0800 Subject: Fwd: [modeller_usage] a question on MODELLER usage I guess how these users' questions and your reply turns to my personal email. I appreciate your feedback as soon as possible. Or would you please check your system kernel of your server, or perhaps it's just a personally operating mistake? sincerely yours, snailliujun ---------- Forwarded message ---------- From: Modeller Caretaker <modeller-care(a)salilab.org> Date: 2008/7/18 Subject: Re: [modeller_usage] a question on MODELLER usage To: Ivan Anishchenko <anishchenko.ivan(a)gmail.com> 抄送： modeller_usage(a)salilab.org Ivan Anishchenko wrote: > I deal with a peptide (35 residues long). I know its amino acid sequence > and a set of mean values for phi- and psi- dihedrals and the respective > confidence interval for each dihedral angle. The data is obtained from > the NMR experiments. The aim is to obtain a structure with the > main-chain dihedrals lying within the corresponding confidence interval > for every residue. Side chains can take any conformation. How can such > restraints be described in MODELLER? 1. Read in the initial structure (see the manual for complete_pdb) or build an extended chain from the AA sequence (model.build_sequence). 2. Add restraints on each dihedral. See Restraints.add. To get the list of atoms for each dihedral type in each residue, see Residue.phi and Dihedral.atoms. For example, to constrain every phi angle in the model 'm' to 0 +/- 0.1 radians, using a Gaussian restraint: for res in m.residues: if res.phi is not None: atoms = res.phi.atoms f = forms.gaussian(group=physical.dihedral, feature=features.dihedral(*atoms), mean=0, stdev=0.1) m.restraints.add(f) 3. You may also want to build other sets of restraints, for example stereochemical restraints. See Restraints.make. 4. Optimize the structure. See conjugate_gradients(). Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage -- Tomorrow is another day. -- Tomorrow is another day.

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a question on MODELLER usage
by Ivan Anishchenko 22 Jul '08

22 Jul '08

Hello, I deal with a peptide (35 residues long). I know its amino acid sequence and a set of mean values for phi- and psi- dihedrals and the respective confidence interval for each dihedral angle. The data is obtained from the NMR experiments. The aim is to obtain a structure with the main-chain dihedrals lying within the corresponding confidence interval for every residue. Side chains can take any conformation. How can such restraints be described in MODELLER? Thanks beforehand! -- Yours sincerely, Ivan V. Anishchenko

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Installation on Debian Linux
by Francesco Pietra 22 Jul '08

22 Jul '08

As a Debian Linux user I found difficult to abandon the Debian packaging system. Therefore, to Install Modeller 9v4-1 I first converted the rpm to deb with alien (flags -k --scripts. Then I installed the deb package with dpkg (flag -i). The command reports that the package is installed but requires a password, indicating which configuration file to edit to set the password. That way, you avoid possible blurring of the OS by going through an rpm; deb positions every file at the expected place; you have the modeller command on path; you have full command of packaging in case of installations of new version. If not already posted by other members, it might be useful, though I understand that Debian (curiously) is not popular in USA. Cheers -- Dr Francesco Pietra Professor of Chemistry Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594 Palazzo Ducale 55100 Lucca (Italy)

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