Difference between revisions of "Alter"

Latest revision as of 17:01, 23 December 2015

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Iterate

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

Copy (transfer) the color from one object to another

stored.colors = {}
iterate obj1, stored.colors[chain,resi,name] = color
alter obj2, color = stored.colors.get((chain,resi,name), color)
recolor

PYMOL API

cmd.alter(string selection, string expression, int quiet=1, dict space=None)

As explained before, all strings must be explicitly quoted. For example to change all HETATM records to ATOM you should do:

cmd.alter('all', 'type="ATOM"')

@@ Line 1: / Line 1: @@
+#REDIRECT [[iterate]]
 '''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:
@@ Line 56: / Line 57: @@
 </source>
-====Coloring a Viral Capsid by Distance from Core====
+====Copy (transfer) the color from one object to another====
-<gallery heights=350 widths=350>
-Image:Capsid_by_dist.png
-</gallery>
 <source lang="python">
-# create a pseudoatom at the origin; we will
+stored.colors = {}
-# measure the distance from this point
+iterate obj1, stored.colors[chain,resi,name] = color
+alter obj2, color = stored.colors.get((chain,resi,name), color)
+recolor
+</source>
-pseudoatom pOrig, pos=(0,0,0), label=origin
+=== PYMOL API ===
-# fetch and build the capsid
+<source lang="python">
+cmd.alter(string selection, string expression, int quiet=1, dict space=None)
+</source>
-fetch 2xpj, async=0, type=pdb1
+As explained before, all strings must be explicitly quoted. For example to change all HETATM records to ATOM you should do:
-split_states 2xpj
-delete 2xpj
-# show all 60 subunits it as a surface
+<source lang="python">
-# this will take a few minutes to calculate
+cmd.alter('all', 'type="ATOM"')
-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>