Hi Horacio, There are several ways of doing this. In a .pml script or on the command line you can do:
/for i in range( 1, 641 ):\ cmd.load( "2jnk%d_rec.mol2" % i, "temp", format="mol2", state=1 )\ cmd.align( "temp", "ref" )\ cmd.save( "2jnkp%d_rec.mol2" % i, "temp", format="mol2" )\ cmd.delete( "temp" ) I'm not entirely sure whether pymol writes mol2, otherwise you can use "mol" or "pdb" (which will be inferred correctly from the extension, by the way). Another possibility is writing a Python script to be called from Pymol (actually, the above is pymol inline python code). Hope it helps (and hope it works :p), Tsjerk On Feb 20, 2008 11:00 AM, Horacio Emilio Pérez Sánchez <horacio.sanc...@int.fzk.de> wrote: > Hi, > > I have 640 very similar protein structures in .mol2 format, named > 2jnk$i_rec.mol2 where $i is the protein number. I need to align all them > respect to the first protein (2jnk1_rec.mol2) and then save separately > each new aligned protein with a different name, for instance > 2jnkp$i_rec.mol2. > > I guess that this can be done using pymol scripts but I have no > experience with this (but from today on I will start to study). Do you > know some method or have some script for this ? Or where to look for > information ? > > Thanks > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
