Re: [ccp4bb] loop modelling?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: loop modelling?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-11-01

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Subject: Re: loop modelling?
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-11-02

Subject: Re: loop modelling?
From: "van den Bedem, Henry" vdbedem {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2009-11-01

Tommi,

If you don't have density, LoopTK is a C++ library with
robotics-inspired algorithms that allows you to generate a large number
of clash-free conformations: https://simtk.org/home/looptk.

Henry

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Pavel Afonine
Sent: Sunday, November 01, 2009 1:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] loop modelling?

Hi Tommi,

if the map shows some density for that loop, I would try two programs
(those I'm familiar with):

1) phenix.fit_loops (need to have PHENIX for this):
http://www.phenix-online.org/documentation/fit_loops.htm
http://www.phenix-online.org/

2) Xpleo:
http://smb.slac.stanford.edu/~vdbedem/

Pavel.

On 11/1/09 4:29 AM, Tommi Kajander wrote:
> Dear all
> I was wondering if anyone knows a simple way to generate a missing
> loop (strech of amino acids)
> really in just some simple manner (no fancy minization necessary, of
> course some constraints probably dont
> hurt), just for visualization purposes of further simulations etc....
>
> thanks!
> tommi

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: loop modelling?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-11-01

Next message:
Subject: Re: loop modelling?
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-11-02