Difference between revisions of "Alter"

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(EXAMPLES)
(EXAMPLES)
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===EXAMPLES===
 
===EXAMPLES===
  
* Change chain label and residue index
+
====Change chain label and residue index====
 
<source lang="python">
 
<source lang="python">
 
  alter (chain A),chain='B'
 
  alter (chain A),chain='B'
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</source>
 
</source>
  
* Change van der Waals radius of a given atom
+
====Change van der Waals radius of a given atom====
 
<source lang="python">
 
<source lang="python">
 
alter (name P), vdw=1.90
 
alter (name P), vdw=1.90
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</source>
 
</source>
  
* Renumber the amino acids in a protein, so that it starts from 0 instead of its offset as defined in the structure file.
+
====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">
 
<source lang="python">
 
# The first residue in the structure file for 1cll is 4.  To change this to 0, maybe to match scripts
 
# The first residue in the structure file for 1cll is 4.  To change this to 0, maybe to match scripts
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</source>
 
</source>
  
* Change the b values of all atoms to the distance of the atoms to a reference point
+
====Change the b values of all atoms to the distance of the atoms to a reference point====
 
<source lang="python">
 
<source lang="python">
 
# reference point
 
# reference point

Revision as of 11:20, 29 July 2011

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

Change the b values of all atoms to the distance of the atoms to a reference point

# reference point
x0,y0,z0=[1,2,3]  
# calculate distance values between the reference point and all the atoms
alldist = []
iterate_state 1, yourstruc, alldist.append(((x-x0)**2.0+(y-y0)**2.0+(z-z0)**2.0)**0.5)
# assign distance values to b-factors 
di = iter(alldist)
alter yourstruc, b=di.next()
# visualize the distances
spectrum b, rainbow, yourstruc

SEE ALSO

Alter_State, iterate, Iterate_State, sort