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Difference between revisions of "Alter"
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===DESCRIPTION=== | ===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 are: | + | '''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, | name, resn, resi, chain, alt, elem, q, b, segi, | ||
type (ATOM,HETATM), partial_charge, formal_charge, | type (ATOM,HETATM), partial_charge, formal_charge, | ||
| Line 28: | Line 28: | ||
alter (name P), vdw=1.90 | alter (name P), vdw=1.90 | ||
</source> | </source> | ||
| − | + | Note that is if dots, spheres, mesh or surface representation is used. You have to refresh the view with | |
<source lang="python"> | <source lang="python"> | ||
rebuild | 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> | </source> | ||
===SEE ALSO=== | ===SEE ALSO=== | ||
| − | [[ | + | [[Alter_State]], [[iterate]], [[Iterate_State]], [[sort]] |
[[Category:Commands|alter]] | [[Category:Commands|alter]] | ||
Revision as of 20:07, 22 April 2008
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
alter (chain A),chain='B'
alter (all),resi=str(int(resi)+100)
sort
- Change van der Waals radius of a given atom
alter (name P), vdw=1.90
Note that is if dots, spheres, mesh or surface representation is used. You have to refresh the view with
rebuild
- Renumber the amino acids in a protein, so that it starts from 0 instead of its offset as defined in the structure file.
# 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