Re: [PyMOL] Question about mutagenesis wizard
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 > 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 >> > > -- > 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 -- Got visibility? Most devs has no idea what their production app looks like. Find out how fast your code is with AppDynamics Lite. http://ad.doubleclick.net/clk;262219671;13503038;y? http://info.appdynamics.com/FreeJavaPerformanceDownload.html___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Question about mutagenesis wizard
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 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Got visibility? Most devs has no idea what their production app looks like. Find out how fast your code is with AppDynamics Lite. http://ad.doubleclick.net/clk;262219671;13503038;y? http://info.appdynamics.com/FreeJavaPerformanceDownload.html ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Question about mutagenesis wizard
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 > -- Got visibility? Most devs has no idea what their production app looks like. Find out how fast your code is with AppDynamics Lite. http://ad.doubleclick.net/clk;262219671;13503038;y? http://info.appdynamics.com/FreeJavaPerformanceDownload.html___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
