modeller_usage

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3151 discussions

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/

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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

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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

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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.

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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 | ==========================================================================

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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

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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

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Restraints from SAXS data
by NM Burton, Biochemistry 07 Jul '09

07 Jul '09

Hello, I'm interested in using SAXS data as restraints for model-building, so checked the modeller_usage archives... Back in January 2007 SAXS restraints were described as "still experimental, and so are probably not generally useful right now." Would this still be a fair description? Cheers, Nick ---------------------- Dr N M Burton Department of Biochemistry University of Bristol BS8 1TD, UK +44 117 3312149 nick.burton(a)bristol.ac.uk

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completing incomplete templates
by Steve Seibold 07 Jul '09

07 Jul '09

Hello Modeller I have a newbie question. I have a template structure that is incomplete. There are a couple of segment loops missing. Is it possible to use Modeller to build up the loops if I give it a complete sequence (fasta) and use the template (with missing loops)? The reason I ask is because it was suggested from another web site that Modeller could do this, but I am not convinced that it can. If not, could someone suggest a software package that could do this? Thanks for your response Steve Steve Seibold Research Asst. Professor seibold(a)chemistry.msu.edu 19B Chemistry Building Michigan State University East Lansing, MI 48824 Office 517-355-9715 ext 264

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Modeling large protein sequence having homologues with less similarity.
by Sehrish Batool 06 Jul '09

06 Jul '09

Hello, My target sequence of protein is too large containing more than 1000 amino acids and I found 4 homologues in PDB showing very less similarity i-e. two showing 28% similarity, one showing 24% and last one showing 19% similarity with my target sequence. Also the starting residues of templates have no homology with my target sequence and Modeller has to read from 1st residue of template, that bocomes impossible in this case. So now how can I model my target sequence?

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