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
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234
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
>>> Porto Alegre, RS, Brasil
>>> Tel: +55 51 3308 9938 <tel:%2B55%2051%203308%209938>
>>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>
>
> --
> 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
> Porto Alegre, RS, Brasil
> Tel: +55 51 3308 9938
>
>
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