- modeller_usage - salilab.org

Hydrogen Atom Preservation
by Alexander Parella 23 May '14

23 May '14

Hello! I have been attempting to use Modeller to refine the loops of some generated protein structures. When performing loop refining, Modeller seems to remove all hydrogen atoms from the structure. I have not been able to find any way to change this behavior. Are there any such options? That is, to stop Modeller from removing the Hydrogen atoms from the structures it refines? Thanks for your time, and any help that anyone can provide.

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Should you use multiple pdb files of the same sequence when available for multiple template homology modeling?
by meginir urestal 05 May '14

05 May '14

Hi, Among the proteins exhibiting homology to my sequence of interest is a protein that has been cristallized with three different ligands by the same team. I was wondering if, when faced with this kind of situation, including all three structures in the homology modeling would introduce a bias. Do you think I should pick one of the structures (based on compare.py) or include all of them in my multiple template modeling? meginir,

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Alternate sidechain positions
by meginir urestal 28 Apr '14

28 Apr '14

how does modeller handle alternate sidechain positions in a pdb file?

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Re: [modeller_usage] How do you use MOULDER?
by meginir urestal 28 Apr '14

28 Apr '14

> Hi, > > I was reading the tutorials and one of them cites MOULDER as an iterative > approach to alignment and homology modeling. > The 2003 paper in nucleic acids research says that MOULDER is restricted > to a few users only. > Has MOULDER been implemented in recent MODELLER versions? If not, how can > you use it on the MODWEB server? > > Thanks, > >

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Generate PDB using diheral angles
by Harinder Singh 28 Apr '14

28 Apr '14

Currently i am using the tleap in amber tools to generate a PDB using only dihedral angles. Is it possible to generate a PDB/Model using only dihedral angles and the sequence, just like amber tools. I have read the whole manual, but didn't get anything useful. The only way you can restrain your model is using restrain file .rsr, which i really don't know how to generate from dihedral angles. -- Harinder Singh Senior Research Fellow Dr. G.P.S Raghava Group IMTECH, INDIA.

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(no subject)
by Julian 23 Apr '14

23 Apr '14

Hello everybody, I would like to know how you model helices with a gap or insertion (pi or 310 helices). I noticed that if the gap / insertion is in the middle of the helix, Modeller arranges it quite nicely with the alpha restraint. But how can I solve this problem if the gap / insertion is at the very end of the helix? Thank you for your answers! Julian

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Modeller Parallel work
by Yao, Jianzhuang 21 Apr '14

21 Apr '14

?Dear Sir/Madam, I am running Modeller to build 500 homology models for a methyltransferase. Now I am running serial job. Do you think I can run parallel job? Or do you think I can submit the same script for 500 times and I can get the same results with serial job? Thanks a lot! Jianzhuang

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GPCRs and iterative modeling
by James Starlight 19 Apr '14

19 Apr '14

Dear modeller users! Inspired by modeller's iterative tutorial I wounder to know more about MOULDING concept of modelling and its automatics implementation within the modelling scripts. For instance I'm modelling of Rhodopsin-like membrane receptors from GPCR super-family with very slow sequence overlap with the closest templates (up to 20%) so I'm not sure both in automated-generated alignments as well as in the final models. How I could improve quality of both things using iterative concept? Does anybody have experience with the GPCRs modeling ? Best wishes, James

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by Dropbox 18 Apr '14

18 Apr '14

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Modeling muli-chain protein
by Richard W. Harper 18 Apr '14

18 Apr '14

Attached is a python script to build a model from the sequence PfFT on the template 1JCS. The first residue in 1JCS is numbered 55. For the start residue in chain A of 1JCS nothing less than 55 is accepted. However, if I put in 55, it tries to align residue 55 in the pir alignment file with residue 1 in the sequence. I have tried various combinations without success. I really did read the documentation. Please help. Thanks. -- Richard W. Harper Ph.D. Research Professor Indiana University-Purdue University Indianapolis (IUPUI) Department of Chemistry and Chemical Biology 402 N. Blackford Street, LD326 Indianapolis, IN 46202-3274

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