Hi, 'save' will save all atoms by default, not only the visible ones. cat in Linux will surely be more efficient than loading in Pymol and saving, but the question related to alignment. cat doesn't do that for you. So the procedure would be:
load A.pdb,A load B.pdb,B align A,B save AB-aligned.pdb Just one addition, Pymol may reorder the atoms. If this is okay (it won't matter for subsequent displaying), don't bother. Otherwise, before saving you might want to 'set retain_order,on' Cheers, Tsjerk On Jan 26, 2008 11:11 AM, Martin Höfling <martin.hoefl...@gmx.de> wrote: > Am Samstag, 26. Januar 2008 schrieb Lu Lin: > > Hi, Abhi, > > You mean save them separately? Is there some way to save them into one > > file? Thanks!! > > By default, the save command should save all (visible?) atoms. Should be in > documentation of save. Any way you can also make a selection of your two > molecules and save the selection to one file. > > Even if you have two files, "cat" will produce a single file quicker than > loading them into pymol ;-) > > Best > Martin > > ------------------------------------------------------------------------- > 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
