July 2009 - modeller_usage

Regarding energy minimization in modeller
by snoze pa 27 Jul '09

27 Jul '09

Hi, I am using modeller to build some homology model. But I am unable to find any script that can be used to minimize the structure. Is there any script available in modeller that can be used to energy minimize the modeled structure. I try to use the old script, model_energies.py but it give me following error message Traceback (most recent call last): File "model_energies.py", line 41, in ? mdl.generate_topology(aln, sequence=code+'-ini') TypeError: generate_topology() got an unexpected keyword argument 'sequence' How modeller can be used to energy minimize a model structure. I am using current version of modeller. Thank you very much. Sincerely, S

2 1

Re: [modeller_usage] modeling a fragment of the target and template sequences
by bharat lal 21 Jul '09

21 Jul '09

Hi Sir, I was jus modeling the structure of 1fdx protein , taking the target 5fd1 (all these files are already there) but after running the script it closes all of a sudden in between and when modeling for the whole of the template and target sequence .. its giving structure .. So can u tell me where am i going wrong ?? and one more question .. If i am executing the script from the command line .. its not getting executed .. whereas a direct click on the script itself .. executes it .. thereby giving the structure ??? Now whats the problem here also .. Please guide .. Bharat See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/

2 1

Introducing HETATM ligands into models based on multiple templates
by Violetta Kivovich 21 Jul '09

21 Jul '09

Hello, I am trying to create a model of a protein using 3 different templates. The first template covers about 1/3 of the protein, the second covers the central part of the model protein and the third overlaps with the second with an additional extension to cover the c- terminus of the protein. The templates' crystal structures have incorporated metal ions and other ligands, which i would like to transfer into the model. Unfortunately i cannot seem to make this work using the script for introducing HETATM ligands into the model. I have created the alignment file and added '.' into both the template and into the sequence alignment. The PDB has the HETATM ligands at the end of the sequence, so i have added them at the end of the alignment file, as suggested in the manual. However, since three different templates are being used, only parts of which overlap, introducing '.' at the end of the model sequence does not work, because it does not align with the template. On the other hand adding '.' into the model sequence, the way it would align with the template, disturbs the structure, disrupting the alignment with the other templates and causing a break in the peptide. I tried adding gaps for each ligand in the other templates, but this does not help. I have tried creating part of the model with just one template and the aligning sequence from my protein of interest. In that situation the ligands are easily added. Is there any remedy to my problem in modeller that i have not considered? here is the script i am using for introducing HETATM ligands into the model # 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 = '1-78-40-clmpldr4.ali', # alignment filename knowns=('1M55','1U0J','1SXJ'), # codes of the templates sequence = 'B25') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling Violetta Kivovich MD/PhD Candidate G4 vzk102(a)psu.edu

2 1

Re: [modeller_usage] Modeling a structure
by bharat lal 21 Jul '09

21 Jul '09

I am modeling the structure of of leptin protein using template as 1AX8 protein with PDB file starting with the 3rd residue .. and I am getting the following error :- Alignment VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQ PDB IQKVQDDTKTLIKTIVTRINDILDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRN Match * *** Alignment residue type 18 (V, VAL) does not match pdb residue type 8 (I, ILE), for align code 1AX8 (atom file 1AX8), pdb residue number "3", 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 1AX8 Cn u pls help regarding this .. Bharat Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/

2 1

Error query!!
by Cool Hunk 17 Jul '09

17 Jul '09

Dear Ben, as i was trying to refine the loops using dope_loopmodel() method, it has generated following error " check_inf__E> Atom 1 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated." but when i used only loopmodel() method it has generated loop models, is thr any way of handling this error or what does it mean. regards Muhammad

2 1

Modelling Multiple Domains into One Multidomain Construct
by Cihan Aydin 16 Jul '09

16 Jul '09

Greetings Modeller community, I am a complete noob to Modeller and I have read several papers which point to Modeller for homology modeling. My question is in essence "Can it be done using the Modeller?" I have two structures for a multidomain protein (in different conformations) from the different genus in the same family. The system I am looking is also in the same family but different from the two I mentioned above. I have the individual structures for each domain for my system but I don't have the full length structure for my system. I would like to model the individual domains onto the two full length structures from the other genii. In addition, I also want to model the substrate-bound forms of these domains from my system to the full length structures from the other genii, but the full length structures in either case does not contain the substrates. I have x-ray structures for every one of them. So can I use the substrate-bound or substrate-unbound x-ray structures from my model to impose upon the full length structures? If I can, how can I achieve it using Modeller? Also if I read it correctly, Modeller optimizes the structure with MD using the CHARMM potential function in vacuo. Is there a way to incorporate the AMBER potential into Modeller and do optimization in solvated form (e.g. in TIP3P shell)? Finally, I was reading the Eramian et al. paper titled "How well the accuracy of comparative protein structure models be predicted?". Is the trained SVM available somewhere to predict the accuracy? Thank you, -- Cihan Aydin UMass Graduate School of Biomedical Sciences PhD Student @ Schiffer Lab 364 Plantation St. LRB 970M Worcester, MA 01605 cihan.aydin(a)umassmed.edu +1 (508) 856-3430

2 1

the pdb template has a break in the chain
by Shawna Frazier 16 Jul '09

16 Jul '09

Hi, I am having an issue where the pdb template contains a chain break but the model I produce is not broken. The pdb template I am using (2bg9.pdb) is already an oligomer with subunit chains denoted by " / ", but each subunit chain is missing a considerable stretch of sequence (the intracellular portion) so each subunit chain is broken into two pieces in the structure. My resulting model structure, however, is not broken. Is there a way I can add a command to break the bond in my model? Thanks.

2 1

Re: [modeller_usage] import site failed
by Mensur Dlakic 16 Jul '09

16 Jul '09

Lixia, It's just a warning, so ignore it and let the program finish modeling. Take care, Mensur At 02:09 PM 7/16/2009, Lixia Jin Day wrote: >I did run Modeller successfully last year. I just cannot figure out what >the problem is now. Every time when I submit a job, it tells me: 'import >site failed use -v for traceback' > >I uninstalled the older version on my computer and installed a recently >version v7 and did testing, and still the same problem. > >I am running on WIndows XP. > >Can anyone tell me what I should do? Thanks! > >Lixia >_______________________________________________ >modeller_usage mailing list >modeller_usage(a)salilab.org >https://salilab.org/mailman/listinfo/modeller_usage ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | Lab: (406) 994-6237 | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

1 0

import site failed
by Lixia Jin Day 16 Jul '09

16 Jul '09

I did run Modeller successfully last year. I just cannot figure out what the problem is now. Every time when I submit a job, it tells me: 'import site failed use -v for traceback' I uninstalled the older version on my computer and installed a recently version v7 and did testing, and still the same problem. I am running on WIndows XP. Can anyone tell me what I should do? Thanks! Lixia

3 2

Adjust weight of homology restraints
by Nick Burton 09 Jul '09

09 Jul '09

Hello, Is it possible to alter the weight of homology-derived restraints, in the same way you can scale other contributions to the energy function (with 'environ.schedule_scale')? I would like to globally down-weight homology-derived restraints to place more emphasis on geometry/electrostatics etc. Any advice would be much appreciated, as was the information on SAXS restraints. Cheers, Nick ---------------------- Dr N M Burton Department of Biochemistry University of Bristol BS8 1TD, UK +44 117 3312149 nick.burton(a)bristol.ac.uk

2 3