AMBER Archive (2002)

Subject: a question about carnal

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Wed Aug 14 2002 - 11:39:36 CDT

I have the following script:

FILES_IN
   PARM p1 wild_type.top;
   PARM p2 com_ra14_ap.top;
   STREAM s1 p2 com_ra14_ap_0.pdb com_ra14_ap_o.pdb;
   STATIC ref p1 wild_type_0.pdb;
FILES_OUT
   TABLE t rms_mol.dat;
   COORD c fit_mol.pdb PDB;
  
DECLARE
   GROUP g1 (RES 1-138 , 140-142);
   RMS fit FIT g1 s1 ref;
  
OUTPUT
   TABLE t fit;
   COORD c fit;
  
END

As you can see I am rms fitting two structures of one kind (p2) to
similar parts of other structure (p1). I would like to see how each of
p2 structure overlays on the p1 structure. In other words I would like
to see bothe p1 and p2 structures in one image. Would you be so kind to
telll me how could I output the coordinates in such a way? I also have
to say that the 2 structure differ only in 1 residue.
Thanks a lot,
vlad
   

-- 
Vlad Cojocaru 
Max Planck Institut for Biophysical Chemistry 
Deparment: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de