Hi James, > As I've understood there are no posible ways to represent H-bonds in > proteins in explicit manner. So I'm looking for possible way to do it > via some plugin or another way.
PyMOL can find polar contacts and represent them as dashed lines. You don't need any extra plugin. http://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts It's the "distance" command with mode=2 that does the job. http://pymolwiki.org/index.php/Distance There are various dash_* settings that control the appearance of the dashed lines: http://pymolwiki.org/index.php/Dash_Length http://pymolwiki.org/index.php/Dash_color (and many others...) > In particular I need > 1) to visualize H-bonds in some structural motifs like coiled coil wich > are dimers of alpha helices ( so I'd like to see H-bonds beetwen > separate alpha helices ) Try this (lets say helix 1 is resi 1-100 and helix 2 is resi 101-200): # add hydrogens (if not already present) h_add donors # detect polar contacts distance hb_coiled_coil, resi 1-100, resi 101-200, mode=2 > 2) to visualize H-bonds in spicified SS structure ( e.g during formation > of the alpha helices)- so I'd like to see H-bonds beetwen amide and > Carboxy groups in specified amino acid sequence. just like example 1, but with other selections: distance hb_backbone, name O, name N, mode=2 > 3) Finally I'd like to check H-bond in protein-ligand complex ( beetwenn > specified ligand groups as well as some amino acid residues of the > ligand binding pocket) just like before, but with ligand as selection 1 and receptor as selection 2. Hope that helps. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ 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
