November 2009 - modeller_usage

Disulfide
by Joel Tyndall 04 Nov '09

04 Nov '09

Hi there, I am building relatively simple models and I have added in my own DISU patch as per the recommended method via FAQ. The disulfide is formed but the dihedrals don't look correct (~150 degrees). Is there something I am missing? (Do I need to add in a larger refinement factor? I am using mod9v7 Cheers Joel Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034

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Tutorial, Advanced example
by Marco 03 Nov '09

03 Nov '09

Hi, I still have a question on the Tutorial. In the Advanced example some news structures are used to improve the model using multiple alignment. But some of this, like 1b8p, are already present in the Basic example and discarded...This is not very clear, at least for me.... :-) Thanks for your help, Marco

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Modeling ligands in the binding site
by Qinghua Liao 03 Nov '09

03 Nov '09

Hi Modeller users, I have a problem of Modeling ligands in the binding site, I have read the manual online, but I still can't understand exactly! my question is what the differences of alignment between that of with and without ligand! Is it just the value of env.io.hetatm? And how to set the atoms with restraint? Could somebody share the all python scripts used during the entire process of Modeling ligands in the binding site? Any response will be highly appreciated! All the best, Qinghua Liao

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Basic tutorial
by Marco 03 Nov '09

03 Nov '09

Dear all, I'm following the basic tutorial and I have a couple of question: a) some times ago Modeller grouped similar structures and scanned against the representative protein of each group: is this still valid? b) where I find the data on cristallografic resolution of the chosen proteins? The pdball.pir file does not contain this data. Thanks for your help, Marco

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(no subject)
by Steve Seibold 03 Nov '09

03 Nov '09

Hello Modeller I believe I figured out the problem with the on-line tutorial. In the tutorial on-line in writes in the python script: env.io.atom_files_directory = ['.', '../atom_files'] However, I got it to work with only with: env.io.atom_files_directory = './:../atom_files' At least I hope this is the answer. Thanks, Steve

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(no subject)
by madhavi choudary 02 Nov '09

02 Nov '09

"bunny.bindumadhavi(a)gmail.com" is ma email id -- m@d#@v|

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(no subject)
by Steve Seibold 02 Nov '09

02 Nov '09

Hello I have been doing the tutorial http://salilab.org/modeller/wiki/Missing%20residues I have generated the alignment.ali file containing the pdb file 1qg8 and the 1qg8_fill sequences. (I basically copied them from the web site). I have gotten "automodel" to work without any problems. However, when I try run "loopmodel" it fails. Again, I am using the script directly from the web site for loop modeling (attached). When I attempt to run it, Modeller loads it libraries etc but then fails with the following error printed, not in log, but to the screen. File "loop-refine.py", line 19, in ? a.make() Does anyone have any insights as to what I could be doing incorrect? Thanks, Steve

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