May 2015 - modeller_usage

Problem with Flex-em fitting
by Sushree Tripathy 28 May '15

28 May '15

Hi, I am trying to use flex-em using modeller 9.15. It is working fine with files given in tutorial. But I have got a structure with 4 chains and a corresponding cubic density map. 1. Now if I am using the rigid.txt file as #helix #chain A 4:A 11:A Then I am getting the error: KeyError: 'No such residue: 4:A' 2. If I am using the rigid.txt as #helix #chain A 4 11 then I am getting the error: if resnum[-1] == 'nr': IndexError: list index out of range 3. If I a, using the rigid.txt as #helix #chain A 4 11 nr then I am getting the error: _modeller.ModellerError: select__690E> Atom index 25 is in multiple rigid bodies! 4. If I a, using the rigid.txt as #helix #chain A 4:A:11:A: 14:A:21:A: then I am getting the error: list.add(mdl.residue_range(resnum[i], resnum[i+1])) IndexError: list index out of range Please let me know what is the correct format of rigid.txt file for multiple chains. One more thing is my PDB contains 4 chains. So where can I give rigid bodies to all of them. Is it the no of iterations in flex-em.py file ? Any suggestion is welcome. Please help. Thanks Sushree.

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Molecular Dynamic Simulation
by shazia sabir 26 May '15

26 May '15

Hi, Does MODELLER has option for molecular dynamic simulation of protein? I got model of query protein from FGF23 wild type using as template. Next I have to see changes because of the single amino acid change at a position. I have to see the interaction of molecule with it receptors after mutation. Can I use MODELLER for this purpose? For closer look at its molecule plus its interaction with receptor? Regards, Shazia.

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Fwd: Regarding modelling of dimer
by Bhavik Sawhney 26 May '15

26 May '15

Dear Sir, This is your post regarding modelling of the dimer protein on dimeric template. I have done the required changes in the ali file (alignment file), do I need to change the PAP file also, because I am getting following error while running Script 4 : Number of residues in the alignment and the pdb files are different. With Regards, Bhavik Hi, If you have a dimer as template and want to model a dimer with the same organisation, you just need to include a "/" character as chain breaker in the alignment file (between your 2 monomers). I join an exemple of alignment for a dimer. On Thu, 12 Jun 2003, Difei Wang wrote: > Hi, All > > I am wondering if it is possible to model a dimer structure from a dimer > template. > I can not find anything in the manual. I tried to model each of them first and > then > put them together. However, I am not sure it is good or not for the packing in > the > contact region. Thanks for your help. > > Difei >

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prepartion input file for modeller
by m_deghan1361 20 May '15

20 May '15

Hi every body I used modeller 9.12 to create a complete pdb file, I have one qeustion: after finding a suitable template by protein blast, should I upload a complete fasta of templete to create PIR file or fasta sequence of templete resulting from blast? I am looking forward to getting your answer thanks a lot best wishes

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Modeller 9.15 release
by Modeller Caretaker 19 May '15

19 May '15

The new version of Modeller, 9.15, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.15 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.15 is primarily a bugfix release relative to the last public release (9.14). Major user-visible changes include: # Warn if 'structureX' is mistyped in alignment file header. # The "RTF restraint not found" warning is now suppressed for the common case of failing to make a peptide bond (and the associated improper) to the next residue at the end of a chain. # Suppress making peptide bond (and the associated improper) to HETATMs unless they appear to be modified amino acids (they have a carbon CA atom). # Bundled version of HDF5 updated to 1.8.13. See the Modeller manual for a full change log: http://salilab.org/modeller/9.15/manual/node40.html If you encounter bugs in Modeller 9.15, please see http://salilab.org/modeller/9.15/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. 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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default optimization and refinement protocol
by CARLOS ARTURO CARVAJAL ARIAS 06 May '15

06 May '15

Hello. I would like to know the parameters of the default optimization and refinement protocol?. I mean, for a.library_schedule is autosched.normal and a.repeat_optimization=1, but for a.max_var_iterations, a.md_level, a.max_molpdf, what parameters are used? When the template has high sequence identity with the target, what would be the recommended level of optimization and refinement? Thanks.

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modelling part by part
by Debajyoti Dutta 06 May '15

06 May '15

Hi, The protein i want to model has 12 transmembrane helices. The topology of the protein is known from an distantly related protein structure. among the 12 transmembrane domains, 5 trnasmembrane helices structures (each helix separate PDB structure) are known determined using NMR. I wonder if it is possible to model the protein based on the hybrid method (using the structural information available). Thanks for your suggestions and help. Best Debajyoti

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