Difference between revisions of "Alter"

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(Coloring a Viral Capsid by Distance from Core)
(Coloring a Viral Capsid by Distance from Core)
Line 54: Line 54:
 
# visualize the distances
 
# visualize the distances
 
spectrum b, rainbow, yourstruc
 
spectrum b, rainbow, yourstruc
</source>
 
 
====Coloring a Viral Capsid by Distance from Core====
 
<gallery heights=350 widths=350>
 
Image:Capsid_by_dist.png
 
</gallery>
 
<source lang="python">
 
# create a pseudoatom at the origin-- we will
 
# measure the distance from this point
 
 
pseudoatom pOrig, pos=(0,0,0), label=origin
 
 
# fetch and build the capsid
 
 
fetch 2xpj, async=0, type=pdb1
 
split_states 2xpj
 
delete 2xpj
 
 
# show all 60 subunits it as a surface
 
# this will take a few minutes to calculate
 
 
as surface
 
 
# create a new color ramp, measuring the distance
 
# from pOrig to 1hug, colored as rainbow
 
 
ramp_new proximityRamp, pOrig, selection=(2xpj*), range=[110,160], color=rainbow
 
 
# set the surface color to the ramp coloring
 
 
set surface_color, proximityRamp, (2xpj*)
 
 
# some older PyMOLs need this recoloring/rebuilding
 
 
recolor
 
 
</source>
 
</source>
  

Revision as of 12:16, 2 August 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