James, > 1) I want to visualise individual water mollecules wich have moved to the > protein interiour during my MD run. How I could hide all solvent water and > visualise only those water wich are within defined cutoff distance from the > protein ?
You can find buried waters with this script: http://www.pymolwiki.org/index.php/Find_buried_waters. It doesn't select waters within a cutoff of the protein, but by each water's solvent accessibility. > 2) I've compared electrostatic protein- ligand contacts by means of PyMol's > present- ligand sites option. As I've noticed the polar contacts are > visualised as the different object. It's very uncomfortable in case when I > want to compare protein-ligand interactions in two conformations of my > protein by means of GRID mode because the polar interactions from both > conformations as the different objects. So as the result I obtain 4 objects > ( 2 of proteins +2 of polar contacts as the simple distances ) instead of 2 > conformations with the polar distances. Is there any possible way to merge > polar interactions with the protein structures to one object ? No. In PyMOL, the underlying representations of molecules are distances are completely different. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
