- modeller_usage - salilab.org

model coordinate uncertainty
by margot 08 Apr '02

08 Apr '02

Dear modelling community, thanks to Michael Buck for his reply, unfortunately the only one. I would assume that there are many modeling problems where it is inherently impossible to derive at a single "best" set of constraints and consequently a single model best satisfying these constraints. I can't believe that there is no general procedure to derive at some mesure of uncertainty associated with the coordinates of a given residue based on a) degree of conservation among template(s) and target, and, b) the local properties of the fold, and, c) variations in the restriants that follow from a) and b). Any helpful thoughts out there? Michael: I'm not sure that I understand what a correlation between an uncertainty (statistical scatter) and error (systematic bias) tells me, or how the quanity you call "model error" is defined. In my case, the problem is a lot greater anyhow, as precise beginnings and endings of secondary structure motifs in target and template are highly likely to vary substantially (beta fold, low to moderate homology). Cheers, margot

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(OTCBB: WSCH) Special Investment Update
by traiber＠ok.ru 04 Apr '02

04 Apr '02

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List update email
by Bozidar 03 Apr '02

03 Apr '02

Hi again, Sorry about the disclosed list of recipients in the previous email. I hit the wrong button. There in no reason for worry, since the email was send to the modeller_usage people only. Thanks, Bozidar

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Stock
by Bozidar Jerkovic 03 Apr '02

03 Apr '02

Please ignore. Thanks, Bozidar

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Re: CHANGE IN A SUBSCRIPTION POLICY Re: (Fwd) Investors in the Stock Market: QY
by Bozidar Jerkovic 02 Apr '02

02 Apr '02

Dear Radha, No that will not be necessary. If I run into some problematic email addresses I will contact the owners of those individually. Best, Bozidar On 2/4/02 8:57 PM, "RATHNACHALAM_RADHAKRISHNAN(a)Lilly.com" <RATHNACHALAM_RADHAKRISHNAN(a)Lilly.com> wrote: > Dear Bozidar, > > Do we have to "subscribe" again? Thanks. > radha > > > Bozidar Jerkovic <bozidar(a)salilab.org> > Sent by: owner-modeller_usage(a)salilab.org > > 04/02/02 06:52 PM > > To: Allen Smith <easmith(a)beatrice.rutgers.edu>, > owner-modeller_usage(a)salilab.org > cc: modeller_usage(a)salilab.org, Andrej Sali > <sali(a)rockefeller.edu> > Subject: CHANGE IN A SUBSCRIPTION POLICY Re: (Fwd) Investors in > the Stock Market: QY > > > > > Hi all, > > Due to an increased influx of a junk mail that the list has been > experiencing lately I propose that we go from the open to a 'members-only' > list. In addition to closing the list, the subscribers will have to be > manually approved as well. > > If you have any suggestions please feel free to contact me. > > I expect to have everything implemented in a week time, so please try to > ignore the junk mail for that time. > > Thanks for your patience, > Bozidar (list owner) > > > > >

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CHANGE IN A SUBSCRIPTION POLICY Re: (Fwd) Investors in the Stock Market: QY
by Bozidar Jerkovic 02 Apr '02

02 Apr '02

Hi all, Due to an increased influx of a junk mail that the list has been experiencing lately I propose that we go from the open to a 'members-only' list. In addition to closing the list, the subscribers will have to be manually approved as well. If you have any suggestions please feel free to contact me. I expect to have everything implemented in a week time, so please try to ignore the junk mail for that time. Thanks for your patience, Bozidar (list owner)

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model coordinate uncertainty
by margot 02 Apr '02

02 Apr '02

Hello modelling community, ist there any accepted algorithm to generate coordinate uncertainties for homology models (or ensembles of models)? If anyone knows of anything published on that matter I'd be grateful for the reference, as well as unpublished insightful material. And another question: Is there any additional bulletin board dealing with protein (biomolecule) modelling in a broader sense than Modeller usage? thanks, margot

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Investors in the Stock Market: QY
by chrislyne 02 Apr '02

02 Apr '02

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(OTCBB: LMGR) Paves the Way in the Field of Optics
by tsu＠email.itl.net.ua 01 Apr '02

01 Apr '02

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How to start
by Jianchao YAO 30 Mar '02

30 Mar '02

Hi, I am a newer for Modeller. After successfully installing Modeller, I wonder how to start modelling. The questions are as follows: 1: Where can I get that alignment files? Need I convert the sequences in FASTA format into PIR format by hands? 2: Where to write those commands? I mean, in other languages, there are developing environments for programmers to write their own commands,however, I don't know how to do it in Modeller. Many thanks Evan

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