OOps! sorry, forgot a couple of vital lines:
from pymol import cmd
from pymol import commanding
def __init__(self):
cmd.extend('allalign',allAlign)
def allAlign(id='xxxx'):
"""Aligns all models in a list to the
specified model where 'xxxx' is the model id you want to
align all others against. Written by Jules Jacobsen
(jacob...@ebi.ac.uk). Feel free to do whatever you like with this code."""
id = id.lower()
pdbList = cmd.get_names()
for entry in pdbList[:]:
entry = entry.strip()
if entry not in id:
cmd.do('align %s, %s\n'%(entry,id))
cmd.do('zoom %s'%(id))
cmd.do('show cartoon, %s'%(id))
Jules
Jules Jacobsen wrote:
Hi,
I've written a script for aligning all structures loaded against your
structure of choice:
def __init__(self):
cmd.extend('allalign',allAlign)
def allAlign(id='xxxx'):
"""Aligns all models in a list to the
specified model where 'xxxx' is the model id you want to
align all others against. Written by Jules Jacobsen
(jacob...@ebi.ac.uk). Feel free to do whatever you like with this code."""
id = id.lower()
pdbList = cmd.get_names()
for entry in pdbList[:]:
entry = entry.strip()
if entry not in id:
cmd.do('align %s, %s\n'%(entry,id))
cmd.do('zoom %s'%(id))
cmd.do('show cartoon, %s'%(id))
just save the section above as a seperate file ie allalign.py and put it
in the PyMOL\modules\pmg_tk\startup directory.
the script is run using the command 'allalign x' where x is the model
you wish to align all others against.
This is one of my first teetering steps into Python so if anyone can
suggest a better way of writing it i'd be keen to hear....
Jules
Douglas Kojetin wrote:
Thanks for that one; it works as advertised.
Another question: if I have 10 different structures read into PyMOL,
what is the best (most accurate) method for aligning the structures as
an ensemble? Currently, I'm aligning all to the first structure read
in (i.e. 2>1, 3>1, etc.) using a for loop and the 'align' command.
Since the structures have different sequences, I cannot use
'intra_fit', etc., is that right? Are there any other commands or
methods of aligning that might be easy to script?
Thanks,
Doug
On Jan 20, 2005, at 2:12 PM, Warren DeLano wrote:
Doug,
Setwise logical ANDs and ORs are tricky at first. In this case, you
want to
create a new set that contains atoms in a1 *or* a2. There aren't any
atoms
that are in both a1 and a2 which is why you're ending up with an empty
object.
create one, a1 or a2
-----Original Message-----
I'm having some problems with selection syntax w/ multiple objects.
I've loaded four different PDB files (in sequence & structure):
load 1.pdb, a1
load 2.pdb, a2
load 3.pdb, b1
load 4.pdb, b2
I wanted to create two new selections:
one = a1 & a2
two = b1 & b2
I've tried many different combinations of PyMOL selection
syntax, but I cannot get the objects to add to the same
selection (using 'create' or
'select'):
create one, a1 + a2
create one, a1 and a2
create one, object a1 + object a2
create one, a*
From what I've read in the manual, I think these commands
are not working because they actually work to select atoms
that are the same between a1 & a2. The manual says it
'selects atoms included in both s1 and s2'.
Any clues or hints?
Thanks,
Doug
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