i have a doubt in this context. while modelling the first model has a least energy what is the necessity for modelling 20 or 50 structures
wrote:
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Today's Topics:
1. restrain beta strands and plates (Arnout Voet) 2. RE: How many models to generate? (Frederico
Arnoldi) 3. Re: RE: How many models to generate? (Charlotte Habegger-Polomat) 4. Re: max number of optima in resdih.lib (Modeller Caretaker)
Message: 1 Date: Fri, 2 Dec 2005 13:53:24 +0100 From: Arnout Voet <> Subject: [modeller_usage] restrain beta strands and plates To: Message-ID: <> Content-Type: text/plain; charset=ISO-8859-1
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
Message: 2 Date: Fri, 02 Dec 2005 13:22:38 +0000 From: "Frederico Arnoldi" <> Subject: [modeller_usage] RE: How many models to generate? To: Message-ID: <> Content-Type: text/plain; charset=iso-8859-1; format=flowed
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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Message: 3 Date: Fri, 02 Dec 2005 10:37:18 -0500 From: Charlotte Habegger-Polomat <> Subject: Re: [modeller_usage] RE: How many models to generate? To: Message-ID:
<> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hello Frederico Arnoldi!
Thanks for your answer...I have been generating 20 models for my protein of interest, and after evaluating the variability within the family of models, I select one or more models to work with.
This reminds me that I have only an "approximation" of my structure, and also allows me to retain some variability. I then work with these models as one would work with a family of NMR structures.
Does anyone else use more than one model to work with after generating a family with Modeller?
Thank you!
-Charlotte Habegger-Polomat
Frederico Arnoldi wrote:
> 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 > >
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Message: 4 Date: Fri, 02 Dec 2005 10:50:59 -0800 From: Modeller Caretaker <> Subject: Re: [modeller_usage] max number of optima in resdih.lib To: Luis Gracia <> Cc: Message-ID: <> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Luis Gracia wrote: > 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
Yes - unfortunately there is a hard-coded limit of 3 optima. This will be removed in the next release of Modeller, but for the time being, you are restricted to 3.
Ben Webb, Modeller Caretaker -- http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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