CCL: How to select residues

 Sent to CCL by: Florian Haberl [Florian.Haberl[A]]
 On Monday 20 March 2006 22:19, Nicolas Ferre nicolas.ferre*
 > Sent to CCL by: "Nicolas  Ferre"
 > Dear CCL'ers,
 > I'd like to select and save a small part of a pdb file. Actually I want to
 > select all the residues inside a given sphere centered on an amino-acid. I
 > know I can use RasMol's "select within (expression)" but it
 results in
 > selecting some atoms, not whole amino-acids. Obviously I can look at the
 > selection using "show selected" and copy/paste every amino-acid
 label, but
 > this is a rather tedious task. Alternatively I can use Molden, but as far
 > as I known, it only shows the corresponding amino-acids without giving the
 > possibility to save them in a file. If I am wrong, please correct me. If
 > not, do you know any free software allowing such residue selection and
 > saving ?
 Also swisspdb viewer ( )   can
 do this:
 Select - neighbors of selected aa:
 Within distance
 If you want to do this with multiple files (for example: You want all aa
 around a ligand),  you can use something like perlmol
 (to be found on: )
 and than the module: midas pattern
 There`s also a solution for python i think its`s called mdtools
 ( )
 and some other molecular toolkits around.
  Florian Haberl
  Universitaet Erlangen/ Nuernberg
  Naegelsbachstr 25
  D-91052 Erlangen
  Mailto: florian.haberl AT