- modeller_usage - salilab.org

Solvation and randomization in ALLOSMOD glycan modeling
by Chakraborty, Srirupa 21 May '19

21 May '19

I am trying to use allosmod package in MODELLER for ab initio modeling of glycans as described in the paper "All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins" (Structures 2013. DOI: 10.1016/j.str.2013.02.004). I have two questions regarding the glycan modeling method, about which I could not find any prior discussions in this forum. My questions are: (1) In the glycan modeling methods section of the paper, it is mentioned that "initial structures were generated by addition of glycan chains with ideal geometries derived from CHARMM, followed by a 1angstrom randomization of the full atomic coordinates". I am assuming this randomization is the same as the randomize_xyz function of MODELLER. However, since templates are not being provided by the user for the glycans, how are the sugar ring puckerings and dihedral angles correctly reproduced even after such large random deviations? (2) My understanding is, in MODELLER, the solvation information is taken implicitly from the template provided. However, since the glycans are modeled template-free, is there any explicit treatment of solvation, or is the optimization done in vacuum? Thanks, -Srirupa

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how to use multiple templates and applying restraints based on one structure.
by Bisignano, Paola 26 Apr '19

26 Apr '19

Hi, I would like to model missing portion of a solved protein structure by using two different templates. I know that is pretty straightforward to use multiple templates, but I would like to include restraints based on the first entry only. Basically I would like to keep the first solved structure as it is, and just move the residues lining the missing portions, while using the second structure as a 'flexible' template. How can I define that I want the restraints based only on the first template? I tried to build a chimera, but I have a bunch of clashes if I do that. Thanks, Paola Paola Bisignano, Ph.D. postdoctoral research associate Department of Pharmaceutical Chemistry Cardiovascular Research Institute University of California, San Francisco

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modeller permission denied
by Almira Ovagimyan 24 Apr '19

24 Apr '19

I'm using modeller 9.21 for Mac and python 2.7.16. I'm trying to run python scripts by using these commands on terminal.However, it gives me permission denied error.How can I solve this permission error? mkdir modeller cd modeller/ ls mod9.21 examples/ Cannot open logfile examples/.log: Permission denied mod9.21 examples/salign/salign_align2d.py Cannot open logfile examples/salign/salign_align2d.log: Permission denied mod9.21 /Library/modeller-9.21/examples/salign/salign_align2d.py Cannot open logfile /Library/modeller-9.21/examples/salign/salign_align2d.log: Permission denied mod9.21 /Library/modeller-9.21/examples/salign/salign_align2d.py >AA Cannot open logfile /Library/modeller-9.21/examples/salign/salign_align2d.log: Permission denied ./run_tests Entering directory: all-steps mod9.21 search.py Cannot open logfile search.log: Permission denied mod9.21 compare.py Cannot open logfile compare.log: Permission denied mod9.21 get-model.py Cannot open logfile get-model.log: Permission denied Entering directory: assessment mod9.21 assess_dope.py Cannot open logfile assess_dope.log: Permission denied mod9.21 assess_normalized_dope.py Cannot open logfile assess_normalized_dope.log: Permission denied <http://aka.ms/weboutlook>

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scoring of the full loop-models
by malkeet singh Bahia 16 Apr '19

16 Apr '19

Hello, In the loop refinement process, is the DOPE score reported only for the refined region or full protein model? If only for the refined region, is there any 'python code', which could be clubbed with loop refinement script to report the DOPE scores of the complete protein models as well? *---*Thanks & Warm Regards*---* Malkeet S. Bahia, PhD Post Doctoral Fellow at the lab of Prof. Hanoch Senderowitz PBC Indo-Israel Post-doc fellowship Dept. of Chemistry, Building 211, Room no. 211 Bar Ilan University, Ramat Gan, 5290002, ISRAEL Mobile: +91-9815988501 (India, WhatsApp only) +972-584553434 (Israel number)

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modeller generated protein loop is weird
by malkeet singh Bahia 10 Apr '19

10 Apr '19

Hello all! I am using Modeller to construct a homology model of my query sequence (250AAs) from two template proteins (A: major protein of 225 AAs and B: minor protein of 25 AAs). The overall identity of the query and template is very high (~85%). There is a loop of 20-25 amino acid, which is constructed using the template B. To my surprise, in the final model, the constructed loop of about 20 amino acid is very weird and is folding back into the protein (sandwiched between secondary structure) resulting in numerous clashes. I feel this is unusual. Could anyone suggest me the reason for this and the probable solution as well? Best, *---*Thanks & Warm Regards*---* Malkeet S. Bahia, PhD Post Doctoral Fellow at the lab of Prof. Hanoch Senderowitz PBC Indo-Israel Post-doc fellowship Dept. of Chemistry, Building 211, Room no. 211 Bar Ilan University, Ramat Gan, 5290002, ISRAEL Mobile: +91-9815988501 (India, WhatsApp only) +972-584553434 (Israel number)

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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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