Hi, You can do this with MOLMOL. The official page from Wuthrich's group seems to be no longer supported. You can find it on the web from several other websites. For example: (http://pjf.net/science/molmol.html), ( http://blog.louic.nl/?p=397).
1) SelectAtom '#1:10@CA' (Structure 1, residue 10, atom CA') 2) SetRef (Sets atom as a reference) 3) SelectAtom 'd > 5.0' (selects all atoms with distance more than 5.0 from that particular CA) 4) From the menus: remove all selected atoms. The remaining ones are all atoms with a distance under 5.0. 5) From the menus: write a pdb file of the remaining atoms. Hope this helps, Yannis Dr A.I. Karsisiotis Research Associate Room Y028 School of Biomedical Sciences University of Ulster Coleraine campus Cromore Road Coleraine Co. Londonderry BT52 1SA +44(0)28701 24336 ai.karsisio...@ulster.ac.uk On 17 November 2012 20:04, Rex Palmer <rex.pal...@btinternet.com> wrote: > I would like to specify a target atom in a pdb file and then isolate all > atoms within a given distance of the target. The selected atoms are then to > be placed in a new pdb file. > Any suggestions please. > > Rex Palmer > http://www.bbk.ac.uk/biology/our-staff/emeritus-staff > http://rexpalmer2010.homestead.com >
