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:[email protected]] On Behalf Of Pavel Afonine Sent: Sunday, November 01, 2009 1:53 PM To: [email protected] 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
