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 ------------------------------------------------------------------------------ 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
