February 2019 - modeller_usage

Hybrid-36 Numbering Support in Modeller
by dms305 26 Feb '19

26 Feb '19

Hi, When using the complete_pdb.py script bundled with Modeller to complete PDB 5GJQ, the resulting PDB model has more than 99999 atoms, which leaves atoms with a numerical ID greater than this with IDs "*****" when the PDB is written out to a file. Is it possible to enable hybrid-36 numbering support in Modeller so that these IDs can be used in downstream analysis? Thanks, Daniel

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Re: [modeller_usage] Crash in libmodeller.dll using PDB 6G2J
by Modeller Caretaker 21 Feb '19

21 Feb '19

On 2/20/19 7:35 PM, dms305 wrote: > Thanks for getting back to me. Please find attached a zip containing > three files: the script representing a minimum reproducible example > using this PDB, the PDB itself and the modeller output from the > script. ... > I don't think this is a memory issue as Jonathan suggested - I'm not > seeing any evidence for this on my system. Thanks! I see the problem, and it's fixed now - will be in the next release. Jonathan was sort of right, in … [View More]

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Crash in libmodeller.dll using PDB 6G2J
by dms305 20 Feb '19

20 Feb '19

Hi, I am using the Modeller Python interface to calculate secondary structure and surface accessibility for a number of PDB files. Whilst it works well for most PDBs, there is a crash in libmodeller.dll when using PDB 6G2J which cannot be caught by Python, i.e. the program simply exits with an AppCrash observed in the Windows Event Viewer. My approach is to generate a completed PDB model using the modeller.scripts.complete_pdb function, followed by the model.write_data function method with ‘… [View More]

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Could modeller change query position in result pdb file?
by jb ZHOU 20 Feb '19

20 Feb '19

Dear Modeller creators, Hello, Modeller is one of state-of-the-art homology modeling software and I have already used several years to model three-dimensional structures. Recently, I have a question about modeller result file (pdb file). I would like to use an example to illustrate my question. I used Modeller to model a sequence in UniProt (UniProt Accesion: Q04721), and I only used parts of sequence to model (from 414 to 532), and I want to get the final three-dimensional … [View More]

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DOPE vs molpdf
by Pawel Kedzierski 11 Feb '19

11 Feb '19

Dear Modeller creators and users, I wonder, which of the scoring functions available in Modeller is preferable to choose best models. A similar question was answered back in 2006: https://salilab.org/archives/modeller_usage/2006/msg00214.html but it was related to very different use case (template of very low identity), and the answer omits the relation to molpdf. The modeller documentation on DOPE score and the 2006 DOPE paper say, that it was designed to choose the best model. However,… [View More]

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