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
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,
Hi Rex,
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.
This is simple to do in PyMOL. After loading your structure just use
the mouse to
Hi Rex,
as easy as:
phenix.pdb_atom_selection model.pdb within(3, chain L and resseq 9 and
name CA) --write-pdb-file=cut.pdb
which in the above example selects all atoms within 3 A from CA atom in
chain A of residue number 9, and writes them into cut.pdb file.
Pavel
On Sat, Nov 17, 2012 at
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