- modeller_usage - salilab.org

Single Mutant Script
by Alex Lian 03 Apr '19

03 Apr '19

I have a few questions about the mutant_model script. I am trying to do a single mutation modeling using this script. optimize(s, sched) s.energy() Where S represents a group of selected atoms (Mutation position). If I understand correctly, The optimize function will do a conjugate gradient to the selected atoms to find the local energy minimum. However, after doing the minimization step, the energy function results in a small positive value which is unusual. I also tried selecting the whole structure which is about 300 residues, did the optimized step and energy computing. This time the energy function showed up with an extremely large positive value. Besides this, I tried to compute the DOPE for both nature structure and the whole sidechain refined structure and found that the DOPE for the refined model is even larger than the one for the native structure which made me so confused. Many Thanks, Alex

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Mutant script warning message
by Alex Lian 02 Apr '19

02 Apr '19

Hi, I need some help about the single mutant script. The following is a warning message I found in the log file. generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 900 902 Residues : GLU PTR Is this the problem relate to the version of the CHARMM? Many thanks, Alex

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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 that due to the large size of the model here, you hit a memory limit - but this is an internal Modeller limit (the stack size), not the total memory on your machine. (The offending arrays are now dynamically allocated to avoid exhausting the stack.) As a workaround for now, you can run this calculation on a Linux or Mac machine - only Windows is affected in this instance. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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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 ‘PSA’ and ‘SSM’ separately. Please can you help me to resolve this issue? Let me know if you need any additional information to be able to reproduce the crash. Thanks in advance, Daniel

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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 structures file (pdb file) which the first amino acid number still start with 414 and the last amino acid number is 532. But in fact the first amino acid number in the final pdb file start with 1 (see figure below, GLU's position is 1, but it is 414 in UniProt,). I could write a script to map it manually, but it is very inconvenience, so could modeller (or module in modeller) realize this ? Sincerely, Zhoujb

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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, this value is not printed out by default neither appear in the detailed evaluation of local model problems presented in the tables of restraints violations. The fact that molpdf only is selected as the default score of model quality makes DOPE at little suspicious. I mean, it looks like there was a reason to hide it. In my case, my models are good enough to all have GA341 scores equal to 1, what makes this value useless. Still, molpdf and DOPE do not correlate, so which one shall I consider more important for model choice? I see from my experience that molpdf is rather sensitive to the choice of templates (e.g. the same protein template from X-ray vs NMR can give very different molpdf values of models, with much more restraint violations for NMR). Also, if one is using multiple templates for the same sequence, the molpdf values are closer to ones obtained using single worst template than to using the best one, while DOPE values do not change much. These observations would count against relying on molpdf, but if molpdf is misleading, then the entire verbose analysis of restraint violations from which molpdf is calculated must be equally misleading. Could you share your insight and comments? With regards, Paweł Kędzierski

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Chain ID not output as part of SSM option to model.write_data
by dms305 18 Jan '19

18 Jan '19

Hi, As part of my use of Modeller, I would like to access the secondary structure information for the model. This looks to be achieved using the SSM option to model.write_data, but this produces a file which doesn’t contain the chain identifier. This could be worked around using the first column (integer index) of the file and knowledge of the chains in the PDB, but it seems awkward to have to do this when the PSA option to write_data is able to include the chain identifier. Is there an alternative way to access the secondary structures, or could this be fixed in Modeller to make using write_data easier? Thanks in advance, Daniel

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Modeller 9.21 release
by Modeller Caretaker 11 Dec '18

11 Dec '18

A new version of Modeller, 9.21, is now available for download! Please see the download page at https://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 9.21 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.21 adds support for Python 3.7 and contains a number of bug fixes. See the Modeller manual for a full change log: https://salilab.org/modeller/9.21/manual/node40.html If you encounter bugs in Modeller 9.21, please see https://salilab.org/modeller/9.21/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 https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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How to (partially) override model.patch_ss_templates() ?
by Luca Jovine 28 Nov '18

28 Nov '18

Hello, I am trying to make a model of a disulfide-bonded protein, where some disulfides are the same as in my templates, but some are shuffled. I redefined the shuffled disulfides as described here: https://salilab.org/modeller/9v7/examples/automodel/model-disulfide.py but the models that I get always show the same exact disulfide connectivity of the templates, i.e. redefining special_patches does not seem to override model.patch_ss_templates(). Is there a way to achieve this, so that I can keep some conserved disulfides from my templates but change others? Thanks, Luca ------------------------------------------------------------------------ Luca Jovine, Ph.D. Professor of Structural Biology & EMBO Member Karolinska Institutet Department of Biosciences and Nutrition & Center for Innovative Medicine Medicinaren 25 Neo Blickagången 16, SE-141 83 Huddinge, Sweden E-mail: luca.jovine(a)ki.se<mailto:luca.jovine@ki.se> W3: http://jovinelab.org ------------------------------------------------------------------------ När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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