Hi Gunnar, > I have a quick question about centering different PDB files. Currently I'm working with 4 different PDB files that need to be centered on the 0,0,0 coordinate. Unfortunately, I have not had much success so far since each PDB file opens up in different locations given their own coordinate systems. > > Is there a software (preferably free/opensource) that will allow me to center all the PDBs on the world origin and save them back out? You can do that with the free YASARA View ( http://www.yasara.org/viewdl ). 1) The manual way: Click File > Load > PDB file (make sure that the 'Center' button is *CHECKED* to center the structure at 0/0/0) Click File > Save as > PDB file, select the structure and *UNCHECK* the 'Transform' button to keep the current atom coordinates 2) The automatic way: Run the following macro, e.g. from the command line with yasara center.mcr for id in '1crn','5tim' Clear LoadPDB (id),center=yes SavePDB all,(id)_centered,transform=no This will create the file '1crn_centered.pdb' etc. If you need more details, just contact me off-list. All the best, Elmar -- Elmar Krieger, PhD YASARA Biosciences & CMBI Outstation Austria Neue-Welt-Hoehe 13/b A-8042 Graz Austria/Europe Ww c(@@)c ================()==OUu============ =WHAT IF YASARA knows the answer?!= =----- http://www.yasara.org -----= =- http://www.cmbi.kun.nl/whatif -= ============OOo==================== () () _/ /_