Hi.
I tried a little:
*test1.pml*
# See http://www.pymolwiki.org/index.php/Peptide_Sequence
# See http://www.pymolwiki.org/index.php/propka
reinitialize
cd C:\Users\tlinnet\Desktop
python
for aa in CVGLTSW:
cmd._alt(string.lower(aa))
python end
create pdb1, cys
remove cys
delete cys
save pdb1.fasta, pdb1
###First time
#python
#for aa in ALTWSIK:
#cmd._alt(string.lower(aa))
#python end
#create pdb2, ala
#remove ala
#delete ala
#translate [-6,-15,0], pdb2
#save pdb2.pdb, pdb2
### Second time
load pdb2.pdb
alter pdb1, chain='A'
alter pdb2, chain='A'
rebuild
create pdb3, pdb1
chainresnresi3 = []
chainresnresi2 = []
iterate pdb3 and name CA, chainresnresi3.append([pdb3,chain,resn,resi])
iterate pdb2 and name CA, chainresnresi2.append([pdb2,chain,resn,resi])
#print chainresnresi3
#print chainresnresi2
python
cmd.wizard(mutagenesis)
for i in range(len(chainresnresi2)):
cmd.do(refresh_wizard)
cmd.get_wizard().set_mode(%s%chainresnresi2[i][2])
#print %s%chainresnresi2[i][2]
selection=/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
#print
/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
cmd.get_wizard().do_select(selection)
cmd.frame(1)
cmd.get_wizard().apply()
python end
cmd.set_wizard(done)
translate [10,-25,0], pdb3
*test2.pml*
reinitialize
cd C:\Users\tlinnet\Desktop
fab CVGLTSW, pdb1, resi=1, chain=A
save pdb1.fasta, pdb1
fab ALTWSIK, pdb2, resi=1, chain=A
translate [0,-15,0], pdb2
create pdb3, pdb1
translate [0,-30,0], pdb3
chainresnresi3 = []
chainresnresi2 = []
iterate pdb3 and name CA, chainresnresi3.append([pdb3,chain,resn,resi])
iterate pdb2 and name CA, chainresnresi2.append([pdb2,chain,resn,resi])
print chainresnresi3
print chainresnresi2
python
cmd.wizard(mutagenesis)
for i in range(len(chainresnresi2)):
cmd.do(refresh_wizard)
cmd.get_wizard().set_mode(%s%chainresnresi2[i][2])
#print %s%chainresnresi2[i][2]
selection=/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
#print
/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
cmd.get_wizard().do_select(selection)
cmd.frame(1)
cmd.get_wizard().apply()
python end
cmd.set_wizard(done)
*test3.pml*
reinitialize
cd C:\Users\tlinnet\Desktop
load pdb1.fasta
load pdb2.fasta
translate [0,-15,0], pdb2
create pdb3, pdb1
translate [0,-30,0], pdb3
chainresnresi3 = []
chainresnresi2 = []
iterate pdb3 and name CA, chainresnresi3.append([pdb3,chain,resn,resi])
iterate pdb2 and name CA, chainresnresi2.append([pdb2,chain,resn,resi])
print chainresnresi3
print chainresnresi2
python
cmd.wizard(mutagenesis)
for i in range(len(chainresnresi2)):
cmd.do(refresh_wizard)
cmd.get_wizard().set_mode(%s%chainresnresi2[i][2])
#print %s%chainresnresi2[i][2]
selection=/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
#print
/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
cmd.get_wizard().do_select(selection)
cmd.frame(1)
cmd.get_wizard().apply()
python end
cmd.set_wizard(done)
*pdb1.fasta*
pdb1
CVGLTSW
*pdb2.fasta*
pdb2
ALTWSIK
Troels Emtekær Linnet
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2012/9/14 Maurício Menegatti Rigo mauriciomr1...@gmail.com
Hi Thomas,
thank you for your response. Actually, the modeling part comes later in
the process. First, I need to perform this step in pymol. In fact, it
would facilitate the modeling process.
Sincerely,
--
Maurício M Rigo
2012/9/14 Thomas Holder spel...@users.sourceforge.net
Hi Maurício,
what you describe here is called homology modeling. Although PyMOL has
some modeling capabilities, I'd strongly recommend to use a real homology
modeling tool such as MODELLER to do this.
http://salilab.org/modeller/
Hope that helps.
Cheers,
Thomas
Maurício Menegatti Rigo wrote, On 09/14/12 19:44:
Dear Pymol users,
I'm a begginer with command lines in Pymol. I'm trying to
complete the following task through a pymol script:
1) Write a file named file1.txt with an aminoacid sequence (e.g.
CVGLTUW)
2) Open a .pdb molecule (file2.pdb) with the same number of
residues, but with a different sequence (e.g. ALTWSIK)
3) Write a code where the pymol will pick each residue of the
file2.pdb (I believe that this could be made by the mutagenesis
wizard command) and mutate for the respective aminoacid written in
my file1.txt
4) Save the new filein .pdb format (file3.pdb)
I'll be very greatful for any help!
Thanks in advance,
-- M.Sc. Maurício Menegatti Rigo
Núcleo de Bioinformática do Laboratório de Imunogenética
Departamento de Genética
Instituto de Biociências
Universidade Federal do Rio Grande do Sul - Campus do Vale
Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M
CEP:91501-970 Caixa Postal 15053
