- modeller_usage - salilab.org

HOH
by Adriana Esteves 15 Nov '07

15 Nov '07

Using the scritp model-ligand.py I introduced a ligand in my model, but the waters were no added. Did I omitted anything in the alignment? Can I copy the waters coordinates from de template file to the modelled one and .... I don't know what to do then, but I something can be done!! This is the script and this the alignment # Homology modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile = 'align-ligand.ali', # alignment filename knowns = '1O8v', # codes of the templates sequence = 'EgFABP2') # code of the target a.starting_model= 4 # index of the first model a.ending_model = 4 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling C; >P1;1O8v structureX:1O8v:1 :A :134 : :EgFABP1 :Echinococcus granulosus: : MEAFLGTWKMEKSEGFDKIMERLGVDFVTRKMGNLVKPNLIVTDLGGGKYKMRSESTFKT TE.S-FKLGEKFKEVTPDSREVASLITVENGVMKHEQDDKTKVTYIERVVEGNELKATVKV DEVVCVRTYSKVA.* >P1;EgFABP2 sequence:EgFABP2:1 : :134 : :EgFABP2:Echinococcus granulosus: : MEPFIGTWKMEKSEGFDKIMERLGVDYFTRKMGNMMKPNLIISDLGDGRYNMRSESKFKT SE-FSFKLGEQFKEVTPDSREVMSMLTVEDGVLKQEQVGKDKTTYIDRVVDGNELRATVKA DELVCVRTYSKRM.* Dra. A. Esteves Secc. Bioquímica Faculty of Sciences Iguá 4225-Montevideo URUGUAY tel.(5982)525 2095 fax (5982)525 8617

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Modeller creating strange structures
by Russell Green 12 Nov '07

12 Nov '07

Dear Modeller community, I have a good structure template to model the missing segment of a protein chain; however, the portion I'm tyring to model should contain a sharp bend. I'm actually using one part of the template for one side of the chain and the other part of the template for the other side of the chain after the bend. When I align the template (wich overlaps with the structure containing the missing portion) the two template pieces look reasonable aside from missing the loop that constitues the bend. After running automodel the template structure is not even retained; instead, it just builds large loops in no particular orientation. Is it possible that the problem is that automodel's constraints make it unable to model the bend correctly? If so, would using the model() class without certain constraints allow me to model this bend? Thanks in advance, Russell Green

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ligand 2
by aesteves＠fcien.edu.uy 12 Nov '07

12 Nov '07

I think I have found the problem but I don´t know how to solve it. The residue in question is an HETATM; I mean that where the sequence indicates a SER the pdb file has an HETATM (CSO). How can I solve it? Thank you ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Fwd: validation and log file
by aesteves＠fcien.edu.uy 12 Nov '07

12 Nov '07

I still worried about validation. I know I have to read the model-default.log file to look for: objetive function and chose the one with the lowest(I did it; the DOPE pseudo-energy value and de value of GA341, and finally the restraint violations, but I did not find the third value and I dont know how to read violations. Can anybody help me to read the log file and find the information I need to validate my model? Thank you very much. Adriana ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- Fin del mensaje reenviado ----- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Writing out chain ID in the PDB
by Vadim Patsalo 12 Nov '07

12 Nov '07

Hello Modeller Users, I am building models in the way described in the basic tutorial. I noticed that the completed model PDB is missing the chain ID column. The template I am modelling from has only one chain, A. Here's an example: Template: ATOM 1 N SER A 2 -6.487 9.533 21.436 1.00 2.23 1SG 2 ATOM 2 CA SER A 2 -5.822 10.328 20.343 1.00 2.86 1SG 3 ATOM 3 CB SER A 2 -6.345 11.788 20.283 1.00 2.67 1SG 4 and model: ATOM 1 N SER 1 -0.662 11.979 19.810 1.00 65.26 1SG 2 ATOM 2 CA SER 1 0.191 12.970 19.122 1.00 65.26 1SG 3 ATOM 3 CB SER 1 -0.325 14.388 19.420 1.00 65.26 1SG 4 Is there a way to force Modeller to print the chain ID? I convert the resulting PDB to charmm format, and some unpleasantness follows because of the missing chain info. Thanks for your help! Vadim -- five.sentenc.es is a personal policy that all email responses regardless of recipient or subject will be five sentences or less. It's that simple.

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ligand
by aesteves＠fcien.edu.uy 10 Nov '07

10 Nov '07

----- Mensaje reenviado de aesteves(a)fcien.edu.uy ----- Fecha: Sat, 10 Nov 2007 11:50:45 -0200 De: aesteves(a)fcien.edu.uy Responder-A: aesteves(a)fcien.edu.uy Asunto: ligand Para: modeller-care(a)salilab.org Hi friends of modeller list: Now, I want to model my protein with a ligand but the program says me that one of the alignment residue does not match with pdb residues. In this site there is a gap in the pdb sequence introduced during alignment since the target has an insertion. The same alignmet file was used to build the model without any problem!! What I have to do? Thank you again, and forgive me for too much questions, but I want to learn how to use Modeller!! Sincerely, Adriana ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- Fin del mensaje reenviado ----- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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symmetry in automodel
by Gordon Wells 06 Nov '07

06 Nov '07

Is it still possible to add symmetry restraints to automodel in spectial_restraints? I used to be able to do this with pick_atoms, but now that "selection" has taken over I seem to be missing something. I define a new class as follows: segsize=??? class sym_model(automodel): def special_restraints(self, aln): sel1 = selection(self.residue_range ('1',str(segsize))).only_mainchain() sel2 = selection(self.residue_range (str(segsize+1),str(2*segsize+1))).only_mainchain() self.restraints.symmetry.append(symmetry(sel1,sel2,1.0)) But get the following output: File "model-dimer.py", line 41, in ? a.make() File "/usr/local/modeller9v2/modlib/modeller/automodel/automodel.py", line 99, in make self.homcsr(exit_stage) File "/usr/local/modeller9v2/modlib/modeller/automodel/automodel.py", line 423, in homcsr self.mkhomcsr(selection(self), aln) File "/usr/local/modeller9v2/modlib/modeller/automodel/automodel.py", line 506, in mkhomcsr self.special_restraints(aln) File "model-dimer.py", line 26, in special_restraints sel1 = selection(self.residue_range('1',str(segsize))).only_mainchain() File "/usr/local/modeller9v2/modlib/modeller/coordinates.py", line 71, in residue_range start = self.residues[start]._num File "/usr/local/modeller9v2/modlib/modeller/coordinates.py", line 183, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/local/modeller9v2/modlib/modeller/util/modutil.py", line 19, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/local/modeller9v2/modlib/modeller/coordinates.py", line 56, in _indxres raise KeyError, ("No such residue: %s" % indx) Thanks in advance -- "He has yet to find out that what's in the public interest is not what the public is interested in." -- The Truth, Terry Pratchett -- Gordon Wells Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria

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Re: [modeller_usage] Transfer_xyz question
by Ali Algarrous 06 Nov '07

06 Nov '07

I'm sorry but it seems I didn't explain myself clearer. What I asked for last time is different than what I'm asking now. This time I want the script to transfer the coordinates for aligned residues only and nothing that is not aligned. So the MSFIEKMIG in my sequance is not going to have any coordinates because it was not aligned with anything from my templae. I hope I explained myself better now. Regards, Ali -----Original Message----- >From Modeller Caretaker <modeller-care(a)salilab.org> Sent Mon 11/5/2007 2:34 PM To Ali Algarrous <algarra(a)uni.edu> Cc modeller_usage(a)salilab.org Subject Re: [modeller_usage] Transfer_xyz question Ali Algarrous wrote: > If i have the following alignment > >>P1;1ji4 > structureX:1ji4:FIRST:A:LAST:A:::: > MKTFEILKHLQADAIVLFMKVHNFHWNVKGTDFFNVHKATEEI---------Y > EEFADMFDDLAERIVQLGHHPLVTLSEAIKLTRV-----KEETKTSFHSKDIF > KEILEDYKYLEKEFKELSNTAEKEGDKVTVTYADDQLAKLQKSIWMLQAHL-- > -----A* > > >>P1;madeup > sequence:madeup::::::: > -------------------------------------------MSFIEKMIGS > LNDKREWKAMEARAKAL---PKEYHHAYKAIQKYMWTSGG--PTDWQDTKRIF > GGILDLFEEGAAEGKKVTDLTGE--D--VAAFCDELMKDTKTWMDKYRTKLND > SIGRD-* > > and i want to transfer the coordinates from my template to my sequence > without building the loops. How should I change my code so it would do > that for me?? What's wrong with the script you posted? Looks like it should do exactly what you want to do to me. And how does your question differ from that at http://salilab.org/archives/modeller_usage/2007/msg00200.html ? I thought that had already been resolved. 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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Asking about energy minimization after initial model]
by Chiranjit Chowdhury 06 Nov '07

06 Nov '07

Dear Friends, I got my initial model for my protein using MODELLER 9v1 which was further assessed by DOPE potential in MODELLER to evaluate model fold and with the program PROCHECK and VERIFY3D. In Ramachandran plot my model showed 93.9% core 5.8% allow .0% gener .3% disall region and 3 bad contacts. Verify 3d data showed above 90% of the residues had an averaged 3D-1D score > 0.2. Please suggest whether I shall have to do energy minimization and if energy minimization is necessay also suggest how it is possible and which parameter I shall have to use for energy minimization. Best regards. -- Chiranjit Chowdhury Department of Biotechnology Indian Institute of Technology, Kharagpur West Bengal, India PIN: 721302

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Transfer_xyz question
by Ali Algarrous 06 Nov '07

06 Nov '07

Hello, If i have the following alignment >P1;1ji4 structureX:1ji4:FIRST:A:LAST:A:::: MKTFEILKHLQADAIVLFMKVHNFHWNVKGTDFFNVHKATEEI---------Y EEFADMFDDLAERIVQLGHHPLVTLSEAIKLTRV-----KEETKTSFHSKDIF KEILEDYKYLEKEFKELSNTAEKEGDKVTVTYADDQLAKLQKSIWMLQAHL-- -----A* >P1;madeup sequence:madeup::::::: -------------------------------------------MSFIEKMIGS LNDKREWKAMEARAKAL---PKEYHHAYKAIQKYMWTSGG--PTDWQDTKRIF GGILDLFEEGAAEGKKVTDLTGE--D--VAAFCDELMKDTKTWMDKYRTKLND SIGRD-* and i want to transfer the coordinates from my template to my sequence without building the loops. How should I change my code so it would do that for me?? This is the code that i have been using. from modeller import * env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') aln = alignment(env, file='alignment.ali',align_codes=('1ji4', 'madeup')) mdl = model(env) mdl.generate_topology(aln['madeup']) # Assign the average of the equivalent template coordinates to MODEL: mdl.transfer_xyz(aln) # Get the remaining undefined coordinates from internal coordinates: mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') # Write the final MODEL coordinates to a PDB file: mdl.write(file='madeup.pdb') Regards, Ali Algarrous

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