Hi James, > 1- Some of my proteins consist of ligand wich include some of amino > acids from sequence of my protein ( e.g fluorophores in GFP). So I'd > like to assign some residue motif as the ligand group ( e.g Ser Tyr Gly > motif in GFP). How I could do it?
The preset selects hetatoms as ligands, so you could do: select motif, (pepseq SYG) and not (name C+N+O) alter motif, type="HETATM" > 2- In some cases there are relatively long distances between polar > ligand groups and protein's polar residues where H-bond must be formed ( > eg in some cases up to 3.5-3.7 A ). So the default a-> present->ligands > sites-> cartoon does not recognize that long H-bonds. How I could set > the H-bond cutoff distance in the above method? there are several h_bond_* settings that control this. (I recommend http://pymolwiki.org/index.php/Grepset to find settings) For example: set h_bond_cutoff_center, 5.0 set h_bond_cutoff_edge, 4.0 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ 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
