Hi Babban, regarding your questions on peptide building:
> My last doubt is about creating polymers out a given PDB ? > I am studying the fibrils of some proteins and although the structure of > fibril is not know but through some analysis I have come to understand > the region in peptide which is leading to fibrillation. PyMOL has a builder where you can create a peptide with given secondary structure. In the external GUI click on "Builder" on the right and then "Protein" on the left side. You may also check this PyMOLWiki page: http://www.pymolwiki.org/index.php/Peptide_Sequence > I want to be able to create a PDB which has like 4/8/16 monomeric > peptide combined through some BETA PLEATED region(i.e the peptides will > join/aggregate around that region (beta region) of the peptide ) and all > I have is the PDB of the monomeric peptide. As far as I know there's no build-in PyMOL function that sticks together two beta-strands. In editing mode you can freely drag around objects: Right-click, "drag object coords", SHIFT+Middle-Mouse-Drag. More precide movements can be achived with translate and rotate commands: http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures#Translate_or_rotate_individual_objects If this is not precise enough for you and you want real beta-sheet modeling, you should use something like modeller. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey _______________________________________________ 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
