[PyMOL] Fwd: asymmetric transformation matrices

[Tsjerk W. <ts...@gm...>]

Hmm, this should've been replied to the list. The info may be useful to others.

Tsjerk

---------- Forwarded message ----------
From: Tsjerk Wassenaar <ts...@gm...>
Date: Mon, Nov 9, 2009 at 5:02 PM
Subject: Re: [PyMOL] asymmetric transformation matrices
To: Thomas Evangelidis <te...@mb...>


Hi Thomas,

You're not doing what you think you're doing.

> # a function to measure Ca distances of oposite pairs of superimpossed
> chains (the proteins must have the same aa composition)
> def check_for_symmetry(tstruct, qstruct):
>    # align the pair
>    cmd.fetch(tstruct)
You fetch the first structure, which is placed in state 1

>    cmd.extract(pdb2entry[tstruct]+"1", tstruct + " and chain "+
> pdb2entry[tstruct][-1:] + " and not hetatm")
You extract part of that structure, which is removed from the state

>    cmd.fetch(qstruct)
You fetch the other structure, which is also loaded into state 1

>    cmd.extract(pdb2entry[qstruct]+"1", qstruct +" and chain "+
> pdb2entry[qstruct][-1:] + " and not hetatm")
You extract part of that structure

>    print "Aligning "+pdb2entry[tstruct]+"1"+" with "+pdb2entry[qstruct]+"1"
>    cmd.align(pdb2entry[tstruct]+"1", pdb2entry[qstruct]+"1")
>    #cmd.do("cealign "+pdb2entry[qstruct]+"1, "+pdb2entry[tstruct]+"1")
>    # align the symmetric pair

>    cmd.fetch(tstruct)
You fetch the first structure again, but this time it's appended to state 2

>    cmd.extract(pdb2entry[tstruct]+"2", tstruct + " and chain "+
> pdb2entry[tstruct][-1:] + " and not hetatm")
You try to extract chain A again. But that is tried on state 1, while
that state has no chain A anymore. The object is empty!

>    cmd.fetch(qstruct)
Same story for the other object

>    cmd.extract(pdb2entry[qstruct]+"2", qstruct +" and chain "+
> pdb2entry[qstruct][-1:] + " and not hetatm")
Empty object...

Then in the next part you calculate the RMSD of distances in an empty
object (all 0) and the aligned one. That RMSD ends up close to the
actual RMSD from the alignment (restricted on CA atoms: 0.280), for
obvious reasons.

I hope this helps,

Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist