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:[email protected]
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of
> steve Alam
> Sent: Friday, September 24, 2004 8:52 AM
> To: [email protected]
> 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
> [email protected]
>
> ******office*************
> Rm 539 Fulmer Hall
> Office: (509)335-2765
> Lab: (509)335-2762
> NMR Center: (509)335-3005
> FAX: (509)335-9688
>
> FEDEX Address********
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> Washington State University
> Pullman, WA 99164-4660
>
>
