September 2007 - modeller_usage

entangled domains
by Russell Green 03 Oct '07

03 Oct '07

Hello, I'm new to Modeller. I have a protein segment I'm trying to model that consists of 2 domains. This protein has 4 very similar domains; 2 have been resolved and the other 2 have not (the ones I want to model). I go through the motions of aligning the sequences and building the model; however, the 2 domains I modelled are basically entangled. Thus, my question is, how can I keep this from happening (such as specifying a straight link between the domains instead of the current one that loops back, if this is even plausible)? Any suggestions are greatly appreciated. Thank you, Russell Green

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Models from secondary structure and distance constraints alone?
by Andrew D. Fant 28 Sep '07

28 Sep '07

[it appears that I accidentally sent this to the listowner rather than the list. oops. sorry Ben] This may seem like a rather strange question, but is it possible to get Modeller to output a PDB structure based only on secondary structure information and a few distance constraints (primarily dicystene relationships). I realize that without an alignment to a known structure, anything that is generated probably bears little resemblance to reality, but I have a relatively short fragment that isn't significantly related to anything in the PDB, and between the disulfide linkages and a couple other known constraints, there aren't that many ways that it could bend together. Basically, I'm trying to generate a consistent structure that is in a possible conformation that doesn't violate steric boundaries and such, without having to manually generate the coordinates from the helix and sheet parameters. Can anyone make any suggestions? Thanks, Andy

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Modeling of a C-terminal segment
by Bo Yang 28 Sep '07

28 Sep '07

Hello, Modeller: I have a question of modelling the C-terminal region of my target. The protein matches with the crystal structure templates except the C-terminal region (named as C-tail here). I did BLAST search using this segment to against the proteins with known structures at Protein Data Band. It returns a match with a short region of an antibody at 56% sequence identity with the inclusion of 4 gaps. The function of my target protein has nothing to do with antibody. I am not sure if it is reasonable to use the BLAST match results as templates to model the conformation of the C-tail. I have thought to model this C-tail region using the Loop Model in Modeller. There are some concerns here. First, the C-tail contains 24 amino acids. Will this be too long for the loop-model in Modeller? If the length is not the problem, how reliable are the conformations of the segment? Second, the segment is at the C-terminal of the protein. For my understanding, the Loop Model in Modeller requires the N and C terminus of the segment to be fixed. The position of the last residues of the segment will have significant influence on the Loop conformation. Which one is more reasonable, to model this segment based on the sequence homology, or use a loop modelling algorithm? Your help and inputs will be much appreciated! Bo --------------------------------- Check out the hottest 2008 models today at Yahoo! Autos.

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September 70% OFF
by VIAGRA � Official Site 26 Sep '07

26 Sep '07

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_modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1CPG
by DANIEL TAYLOR 25 Sep '07

25 Sep '07

Hello People I know this has been raised before but when looking through the archieves I could'nt find an answer to this problem, I've redone all the tutorials and out of ideas, so please can somebody help with this error message I'm getting? 'import site' failed; use -v for traceback Traceback (most recent call last): File "modeller.top.py", line 18, in ? a.make() # do the actual homology modeling File "/home/fraizerangus/bin/modeller9v2/modlib/modeller/automodel/automodel.py", line 99, in make self.homcsr(exit_stage) File "/home/fraizerangus/bin/modeller9v2/modlib/modeller/automodel/automodel.py", line 399, in homcsr aln = self.read_alignment() File "/home/fraizerangus/bin/modeller9v2/modlib/modeller/automodel/automodel.py", line 389, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/home/fraizerangus/bin/modeller9v2/modlib/modeller/alignment.py", line 74, in append rewind_file, close_file) _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1CPG Many Thanks Dan

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Mutations
by laura.buttazzo＠email.it 25 Sep '07

25 Sep '07

Dear all, I'm a new user of Modeller and I have a question about the model computing. If I take one/or more models with a given alignment and I change just one or more amino acids maintaning the same alignment, should I obtain a different model? In other words, Can Modeller be used for calculating mutations? Thank you so much, Laury -- Email.it, the professional e-mail, gratis per te: http://www.email.it/f Sponsor: Cerchi unauto usata, vuoi vendere il camper o il cellulare? Prova Email.it Annunci, pochi click per pubblicare e trovare ciò che vuoi! Clicca qui: http://adv.email.it/cgi-bin/foclick.cgi?mid=6893&d=20070925

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regarding loop refinement
by simran jeet 25 Sep '07

25 Sep '07

After loop refinement, we get files with .IL and .BL extensions. Which one should be used as the final model out of these? And after refinement through modeler there are some bad contacts and disallowed regions. How can we assess the models accuracy?

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disulfide bonds in aligned structures?
by Mike White 24 Sep '07

24 Sep '07

Hello, I have been modeling a homopentamer which should have a disulfide bond in each subunit in the same position as the multiple templates that we are using (the alignments have the cys residues of the target lined up with the disulfide-forming cys in the templates). When I carry out the alignment of the templates using salign, the XX_fit.pdb files for the templates do not have the disulfides indicated using SSBOND, even though the original pdb files (XX.pdb) do have the SSBOND lines in them. I know that automodel will automatically include disulfide restraints if the templates have them. However,the returned models, while superimposing nicely on the template structure, do not have the disulfides, even though the cysteines in the model are right where the disulfide-forming cysteines are in the template. I assume that automodel uses the XX_fit.pdb files for the fitting routines, and the fact that the XX_fit.pdb files are missing the SSBOND lines is why the disulfides are present in the model. Is this correct? Can I just edit the XX_fit.pdb files to include the SSBOND lines to force the model to have the disulfides? Alternatively, I guess I could use model.patch as per node24 in the online manual to force the disulfides to be where I want them to be, but this just doesn't seem right if the templates all have the disulfide and the alignments have the cysteines where they should be. Thanks Mike White

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(no subject)
by simran jeet 24 Sep '07

24 Sep '07

I have generated models for proteins but dont know how to optimize and refine those structures using modellar. I have tried using the optimize.py file to optimize with CG but i am not able to understand the script and where should I list the protein name to be optimized in that script file.

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help
by huifang liu 24 Sep '07

24 Sep '07

Hello! When I finished inshalling modeller , I typied the command mod9v2. But the computer replied me with the sentance:The command can not found .Can you tell me the reason? Thanks

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