Hi Pymol users,
I posted a question last week (attached below) that didn't generate any
responses so I'm thinking maybe I was being too specific. So I'd like to
restate the problem in a much more general way: I'm trying to apply a
set of shifts sequentially from a numpy array to each atom in the
structure. The basic way I try to do this is:
cmd.load( "../4lzt_quasi.pdb", "full")
cmd.create("anew", "full", 1, 1)
cmd.alter_state(1,"anew" , "x,y,z = x+nm[(ID-1)*3],
y+nm[(ID-1)*3+1], z+nm[(ID-1)*3+2]")
but it seems that the create command changes the IDs of the atoms so
that the shifts are now applied to the wrong atoms (eg a CA atom with
ID=5 has ID=1 in the newly created object).
So the question is:
- does anyone know how and why the ID's are change? (then I could
reorder the shifts in my array to match the new object)
- or is there a better way to apply shifts to the atoms?
Thanks!
Pawel
-------- Original Message --------
Subject: Re: [PyMOL] discrepancy between python and commandline script
Date: Fri, 08 Nov 2013 07:30:28 -0500
From: Pawel <pawe...@gmail.com>
To: Pawel Janowski <pawe...@gmail.com>, pymol-users@lists.sourceforge.net
Hi,
I've continued to investigate and have gotten even more confused. This
script:
from numpy import *
import sys
cmd.delete("all")
cmd.load( "../4lzt_quasi.pdb", "full")
cmd.create("anew", "full", 1, 1)
print "First 3 shifts: ", nm[0:3], "\n"
cmd.alter_state(1,"anew" , "x,y,z = x+nm[(ID-1)*3],
y+nm[(ID-1)*3+1], z+nm[(ID-1)*3+2]")
xyz1=[]
cmd.iterate_state(1, 'full & id 5', 'xyz1.append([x,y,z])')
xyz2=[]
cmd.iterate_state(1, 'anew & id 1', 'xyz2.append([x,y,z])')
print "Coords of full id 5:", array(xyz1)
print "Coords of anew id 1:", array(xyz2)
print "Shift between full id5 and anew id1:",
array(xyz1)-array(xyz2), "\n"
xyz1=[]
cmd.iterate_state(1, 'full & resid 1 & name ca ',
'xyz1.append([x,y,z])')
xyz2=[]
cmd.iterate_state(1, 'anew & resid 1 & name ca ',
'xyz2.append([x,y,z])')
print "Coords of full resid1 name ca: ", array(xyz1)
print "Coords of full resid1 name ca: ", array(xyz2)
print "Shift between full id5 and anew id1: ", array(xyz1)-array(xyz2)
print "\n"
yields:
PyMOL>run pymoltest1.py
First 3 shifts: [-0.1263 0.0152 -0.0444]
Coords of full id 5: [[ 2.539 5.619 12.706]]
Coords of anew id 1: [[ 2.4127 5.6342 12.6616]]
Shift between full id5 and anew id1: [[ 0.1263 -0.0152 0.0444]]
Coords of full resid1 name ca: [[ 2.539 5.619 12.706]]
Coords of full resid1 name ca: [[ 2.4127 5.6342 12.6616]]
Shift between full id5 and anew id1: [[ 0.1263 -0.0152 0.0444]]
What I see from this is:
- the first set of shifts is applied to the CA atom which is the
fifth atom in the original pdb file and somehow becomes the second atom
in the object created with cmd.create
- the object created by cmd.create has atom id's spanning from 0 to
N-1 (original object had atom ids from 1 to N)
I would like to know what is happening but, more importantly, what is
the best way to apply the shifts vector "nm" to the atoms in the
original object where the shifts in "nm" are according to the order in
the pdb file.
Thanks!
Pawel
-------- Original Message --------
Subject: discrepancy between python and commandline script
Date: Thu, 07 Nov 2013 18:55:17 -0500
From: Pawel <pawe...@gmail.com>
To: pymol-users@lists.sourceforge.net
Hello,
I'm trying to understand what seems like an inconsistency between PyMOL
commandline and python scripts. I have the following commandline script:
delete all
load ../4lzt_quasi.pdb, full
cmd.create("anew", "full", 1, 1)
cmd.alter_state(1,"anew" , "x,y,z = x+nm[(ID-1)*3],
y+nm[(ID-1)*3+1], z+nm[(ID-1)*3+2]")
iterate_state 1, full & id 1, print x, y,z
iterate_state 1, anew & id 1, print x, y,z
Which I then run:
PyMOL>@pymoltest1.txt
...
PyMOL>iterate_state 1, full & id 1, print x, y,z
2.69099998474 4.58500003815 13.6999998093
IterateState: iterated over 1 atom coordinate states.
PyMOL>iterate_state 1, anew & id 1, print x, y,z
2.41267466545 5.63420581818 12.6615524292
IterateState: iterated over 1 atom coordinate states.
Now I have this python script:
cmd.delete( all)
cmd.load( "../4lzt_quasi.pdb", "full")
cmd.create("anew", "full", 1, 1)
cmd.alter_state(1,"anew" , "x,y,z = x+nm[(ID-1)*3],
y+nm[(ID-1)*3+1], z+nm[(ID-1)*3+2]")
xyz1=[]
cmd.iterate_state(1, 'full & id 1', 'xyz1.append([x,y,z])')
xyz2=[]
cmd.iterate_state(1, 'anew & id 1', 'xyz2.append([x,y,z])')
print xyz1
print xyz2
Which I run:
PyMOL>run pymoltest1.py
[[2.690999984741211, 4.585000038146973, 13.699999809265137]]
[[2.5646746158599854, 4.600205898284912, 13.65555191040039]]
Why am I getting different coordinates for the second atom? The second
set of coordinates from the first script are actually the coordinates of
the 5th atom in my structure (CA of a LYS). I'm guessing that the
alter_state command is somehow doing something different in one and the
other case but it's hard to understand why.
Thanks for the help,
Pawel
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