Steve, Yes, in fact that's currently the only way it can save them. Just use the save command.
You also might think about selections and loops: cnt=22 for a in range(1,cnt+1): \ cmd.load("FINALCNS_%d"%a,"MOL%d"%a) select region, (102-106,112-116,122-135,137-139,141-145,148-149,156-160,166,171/CA,N,C,O) for a in range(2,cnt+1): \ cmd.align("region & MOL%d"%a,"region & MOL1") for a in range(1,cnt+1): \ cmd.save("fit%d"%a,"MOL%d"%a) Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > steve Alam > Sent: Friday, September 24, 2004 8:52 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] saving transformed PDB files > > Dear Pymolers, > > I've been using pymol to superimpose NMR ensembles. The Align > FXN works great and would look something like: > > > load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_1.pdb, > MOL1 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_2.pdb, MOL2 > load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_3.pdb, > MOL3 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_4.pdb, MOL4 > load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_5.pdb, > MOL5 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_6.pdb, MOL6 > load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_7.pdb, > MOL7 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_8.pdb, MOL8 > load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_9.pdb, > MOL9 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_10.pdb, > MOL10 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_11.pdb, > MOL11 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_12.pdb, > MOL12 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_13.pdb, > MOL13 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_14.pdb, > MOL14 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_15.pdb, > MOL15 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_16.pdb, > MOL16 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_17.pdb, > MOL17 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_18.pdb, > MOL18 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_19.pdb, > MOL19 load > /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_20.pdb, MOL20 > > > align > (MOL2///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL3///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL4///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL5///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL6///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL7///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL8///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL9///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL10///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL11///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL12///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL13///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL14///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL15///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL16///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL17///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL18///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL19///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > align > (MOL20///102-106,112-116,122-135,137-139,141-145,148-149,156-1 > 60,166,171/CA,N,C,O), > (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16 > 0,166,171/CA,N,C,O) > > > > My question is how (and IF) can I get pymol to save each file > in the newly transformed coordinates. Is this possible? > > THNX in advance! > > Steve > > Steven L. Alam, Assistant Professor > School of Molecular Biosciences > Washington State University > PO BOX 644660 > Pullman, WA 99164-4660 > a...@wsu.edu > > ******office************* > Rm 539 Fulmer Hall > Office: (509)335-2765 > Lab: (509)335-2762 > NMR Center: (509)335-3005 > FAX: (509)335-9688 > > FEDEX Address******** > Rm 630 Fulmer Hall > Washington State University > Pullman, WA 99164-4660 > >