CCL: Overlay structure

 Sent to CCL by: Daniel Roe [daniel.r.roe|gmail.com]
 Hi,
 If you would like a scriptable way to do this you could use CPPTRAJ,
 part of the freely available AmberTools
 (http://ambermd.org/AmberTools15-get.html).
 For example, if your X-ray structure is called X-ray.pdb and your
 optimized structure is called Opt.pdb, you could use the following
 commands in CPPTRAJ to perform a best-fit alignment and calculate RMSD
 for all CA atoms:
 parm X-ray.pdb
 reference X-ray.pdb
 trajin Opt.pdb
 rms ToRef reference ]_[CA out rmsd.dat
 trajout Aligned.pdb
 go
 The structure of Opt.pdb aligned on X-ray.pdb will be written to
 Aligned.pdb, and the RMSD will be written to 'rmsd.dat'. You can also
 calculate the per-residue RMSD if desired via the 'perres' keyword.
 Hope this helps,
 -Dan
 On Mon, Feb 29, 2016 at 12:34 PM, Saied Mohammed Soliman
 saied1soliman%yahoo.com <owner-chemistry]_[ccl.net> wrote:
 >
 > Sent to CCL by: "Saied Mohammed Soliman"
 [saied1soliman__yahoo.com]
 > Hello colleagues,
 > I need a free and user friendly software to overlay the optimized structure
 > with the X-ray structure in order to compare the matching between them,
 > anyone could help me.
 > Thanks
 > Saied>
 >
 --
 -------------------------
 Daniel R. Roe, PhD
 Department of Medicinal Chemistry
 University of Utah
 30 South 2000 East, Room 307
 Salt Lake City, UT 84112-5820
 http://home.chpc.utah.edu/~cheatham/
 (801) 587-9652
 (801) 585-6208 (Fax)