Hi Martin & James, is it just a coincident that you both ask almost the same question?
You could remove all water atoms with few protein contacts or with a small surface area. For example: remove solvent beyond 3.5 of polymer set dot_solvent get_area solvent, load_b=1 remove solvent and b > 20 Hope that helps. Cheers, Thomas On 04/26/2012 10:55 AM, James Starlight wrote: > Another question- I have my protein.pdb with some inserted crystall > waters within protein interiour as well as water surrounded of my > protein. I want to remove only sorrounding water but prevent internal > water ( wich could be functional relevant ). > > How I could to select such surrounded water ( e.g via some cutoff > radius relative my protein etc) wich I'd like to remove further ? On 04/25/2012 05:34 PM, Martin Hediger wrote: > In a crystal structure, there are usually a number of relevant crystal > waters, as well as water molecules on the surface. In our approach, we > model the protein structure within a dielectric continuum, so surface > water molecules are not required (to save computer time). However, > waters in the interior should remain in our model. How could we discard > the surface waters while keeping the internal waters? -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ 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
