- modeller_usage - salilab.org

GPCR modeling
by Sharangdhar S. Phatak 07 Aug '08

07 Aug '08

Hello, I was wondering if anyone could help me address the issue of flipped residues. I am modeling a 7-TM GPCR and in one of the TM the residues are flipped. Is there a way to fix this? Thank you Sharang

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new to modeller
by Chinwe Ekenna 02 Aug '08

02 Aug '08

good day sir, pls i'm new to modeller and do not know where to start .i have read the manual but it get all confusing . i have not put in any input file cos i don't know where to start. i tried running the modeller mod9v3 model-default.py and it gives me import site failed cannot open file or directory . please help. if i can know the very first thing to do i think i can take it from there. thank you in advance chinwe

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Oligomer Modelling
by Manjunatha Karpenahalli 31 Jul '08

31 Jul '08

Dear All, Is it possible to model home-tetramer using modeller? Thank you very much in advance. Download prohibited? No problem. CHAT from any browser, without download. Go to http://in.webmessenger.yahoo.com/

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build_profile.log?
by Μαρία Τζιαστούδη 31 Jul '08

31 Jul '08

Hi, could anyone help me? I don't understand if a template was found for my two sequences.

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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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