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:[log in to unmask]] On Behalf Of
Pavel Afonine
Sent: Sunday, November 01, 2009 1:53 PM
To: [log in to unmask]
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
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