RE: [PyMOL] distance sequence output

[DeLano, W. <wa...@su...>]

> From: Kristian Rother=20

> In this and other recent questions inside and outside this=20
> forum i have=20
> discovered that many of them could be solved quite easy if=20
> there was an=20
> easy way to access the atomic coordinates directly from the PyMOL API.
>=20
> Is this achievable somehow?

The actual C-langauge arrays aren't exposed, but there are at least =
three different ways you can modify coordinates from within Python:

#####=20
(1) You can get a python object which contains the molecular =
information, modify the coordinates in that object, load the modified =
molecule into PyMOL, update the modified coordinates to the original =
model, and then delete the modified object.

(in a python script)

from pymol import cmd

model =3D cmd.get_model("pept")
for a in model.atom:
   a.coord=3D[ -a.coord[1], a.coord[0], a.coord[2]]

cmd.load_model(model,"tmp")
cmd.update("pept","tmp")
cmd.delete("tmp")

######
(2) Another approach is the "alter_state" function, which can perform =
the same transformation in a single PyMOL command statement:

alter_state 1,pept,(x,y)=3D(-y,x)

Likewise sub-selections can be transformed as well:

alter_state 1,(pept and name ca),(x,y,z)=3D(x+5,y,z)

#######
(3) A third approach is to use alter_state with the global "stored" =
object:

(in Python script)

from pymol import cmd
from pymol import stored

stored.xyz =3D []
cmd.iterate_state(1,"pept","stored.xyz.append([x,y,z])")

# at this point, stored.xyz is a native Python array holding
# the coordinates, which you can modify as required

stored.xyz =3D map(lambda v:[-v[1],v[0],v[2]],stored.xyz)

# and now you can update the internal coordinate sets

cmd.alter_state(1,"pept","(x,y,z)=3Dstored.xyz.pop(0)")

#####

Approaches 2 gives the best performance, approach 3 gives more =
flexibility, and approach 1 gives you a reusable and fully modifiable =
Python object.

Cheers,
Warren