CCL: How to select residues



 Sent to CCL by: Florian Haberl [Florian.Haberl[A]chemie.uni-erlangen.de]
 hi,
 On Monday 20 March 2006 22:19, Nicolas Ferre nicolas.ferre*univ-provence.fr
 wrote:
 > Sent to CCL by: "Nicolas  Ferre"
 [nicolas.ferre]^[univ-provence.fr]
 > 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 ( http://www.expasy.org/spdbv/text/download.htm )   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: http://www.perlmol.org/ )
 and than the module: midas pattern
 There`s also a solution for python i think its`s called mdtools
 (http://www.ks.uiuc.edu/Development/MDTools/ )
 and some other molecular toolkits around.
 Greetings,
 Florian
 --
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  Florian Haberl
  Computer-Chemie-Centrum
  Universitaet Erlangen/ Nuernberg
  Naegelsbachstr 25
  D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de
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