December 2005 - modeller_usage

restrain beta strands and plates
by Arnout Voet 02 Dec '05

02 Dec '05

dear modellers i have met a problem in my scripting to restrain the secondary structure element beta sheet beta strand. For alpha helices it works and i see an influence on the modelled structure , however for sheets it does not work and i get the same model with or without the restraining in the script. Could somebody pleez help me with the exact restraining of it kind regards arnout voet phd student biochemistry kuleuven. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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Occupancy problem ?
by Nicolas 02 Dec '05

02 Dec '05

Hello everybody, I am trying to use several templates for homology modelleing but some present half-occupancy for some residus of my structures. As soon as I try to modelise my sequence, I get the "structure not read in" message. Is this linked to the occupancy ? I did try the same scripts with a structure which does not present any occupancy uncertainty and it works fine. Thanks Dr. Bischler Nicolas NHRF-IOPC 48a, Vasileos Constantinou 11635 Athens Greece Tel : +302107273895 Fax : +302107273831

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max number of optima in resdih.lib
by Luis Gracia 02 Dec '05

02 Dec '05

Hi! I need to modify the rotamer definitions in resdih.lib, but I get the following error when adding 4 entries to a residue. _modeller.error: rdrdih__223E> Internal error: array too small: MDIHOPT current maximum, current need: 4 4 This is the line that creates the error: CA CB CG OD1 4 0.516 0.194 0.161 0.129 -11.9 69.4 -67.6 154.8 12.5 11.1 23.3 25.7 -180 -90 -90 0 0 90 90 180 using only 3 optima values doesn't give any error. Is there a limit in the maximum number of optima? This info is part of the output but I don't know if its a limit or the number found: Maximal number of dihedral angle optima: 3 Thanks for the help Luis -- Luis Gracia, PhD Department of Physiology & Biophysics Weill Medical College of Cornell University 1300 York Avenue, Box 75 New York, NY 10021 Tel: (212) 746-6375 Fax: (212) 746-8690 lug2002(a)med.cornell.edu

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RE: How many models to generate?
by Frederico Arnoldi 02 Dec '05

02 Dec '05

Hello Charlotte Habegger-Polomat, I am not an expert modeller user, but what I can "share" about it? I think the number of models generated depends on available time and computational power you have to carry it. I usually generate between 100 and 200, and select that model with the lowest "current energy". Probably somebody could discuss it better, anyway, I tried ;) Frederico Arnoldi UNESP - Rio Claro - Brazil > >Dear Modeller users, > >I was wondering if others would share how many structures you usually >generate for a family of models. > >I am currently working on modelling my protein of interest with 3 known >template structures (>30% sequence similarity). When using Modeller, I >generate a family of 20 models and then evaluate the variability and >quality of models within the family. > >How many do other Modeller users generate? > >How do you decide on this number? > >I've read articles where 3 models, others where 30 models were generated >with Modeller... > >Thanks! > >-Charlotte Habegger-Polomat

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