Alter

2008-04-22T20:07:00Z

Jkrausuwc:

===DESCRIPTION===
'''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space, which are are explained in [[Iterate]] are:
name, resn, resi, chain, alt, elem, q, b, segi,
type (ATOM,HETATM), partial_charge, formal_charge,
text_type, numeric_type, ID, vdw

All strings must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered.

'''WARNING''': You should always issue a '''sort''' command on an object
after modifying any property which might affect canonical atom
ordering (names, chains, etc.). Failure to do so will confound
subsequent "create" and "byres" operations.

===USAGE===
alter (selection),expression

===EXAMPLES===

* Change chain label and residue index
<source lang="python">
alter (chain A),chain='B'
alter (all),resi=str(int(resi)+100)
sort
</source>

* Change van der Waals radius of a given atom
<source lang="python">
alter (name P), vdw=1.90
</source>
Note that is if dots, spheres, mesh or surface representation is used. You have to refresh the view with
<source lang="python">
rebuild
</source>

* Renumber the amino acids in a protein, so that it starts from 0 instead of its offset as defined in the structure file.
<source lang="python">
# The first residue in the structure file for 1cll is 4. To change this to 0, maybe to match scripts
# outputted from other programs, just remove the offset of 4 from each atom
alter 1cll, resi=str(int(resi)-4)
# refresh (turn on seq_view to see what this command does).
sort
</source>

===SEE ALSO===
[[Alter_State]], [[iterate]], [[Iterate_State]], [[sort]]

[[Category:Commands|alter]]

PyMOL Wiki - User contributions [en]

Alter