Re: [ccp4bb] Superposition of maps from different crystal forms

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 27 April 2007

Previous message:
Subject: Re: Structures with pseudo-uridine?
From: Poul Nissen pn {- at -} MB {- dot -} AU {- dot -} DK
Date: 2007-04-27

Next message:
Subject: Re: Error with scala after combat
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-04-27

Subject: Re: Superposition of maps from different crystal forms
From: Paul Emsley emsley {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-27

Andrew,

Did you try the NCS maps in Coot and it didn't work and therefore
you are going down this rather convoluted route?

On Fri, Apr 27, 2007 at 10:20:12AM +0100, Eleanor Dodson wrote:
> Well - I would do it the same way as you are - find a matrix with
> lsqkab, then apply that to the map with maprot.
>
> It should be OK.
> However there are some tricks which might help. Small differences in
> cell dimensions sometimes muddle coot I think and also I think it gets
> confused by different symmetry in different maps.

Hurmpf! I suspect an error with the cells during the maproting.
... but maybe I am biased.

One more thing, you can do the lsq match in Coot and get a matrix.
You can then apply this matrix to the map in Coot using the
transform-map function (that's how I would do it).

Paul.

>
> 1. This shouldnt matter , but I try to make sure I am using coordinates
> as close to the origin as I can get them - choose the symmetry operator
> to do this.
>
> If you run pdbset xyzin now.pdb
> end
> It gives you the centre of mass of the molecule.
>
> Choose a symmetry operator to apply to move it towards the origin.
>
> Then get the lsqkab matrix for that pair of solutions.
>
> 2. I usually expand the maps to P1, make sure I am reading in a piece of
> map which completely covers the molecule, and only use P1 symmetry in
> coot for that map ( in fact you wont need any symmetry generation )
>
> Eleanor
> Andrew Robinson wrote:
> >Hi all,
> >
> >I could really use some help with the following situation:
> >
> >I have electron density maps of my protein in two crystal forms. The
> >first is the apo form which is in P43212 with a = b = 88.2, c = 159.1.
> >If I soak a substrate for this protein into these crystals, I get a
> >second crystal form in P41212 with very similar unit cell dimensions (a
> >= b = 88.7, c = 158.7). The two forms are virtually identical except
> >that an apparent conformational change causes reverses the handedness of
> >the packing.
> >
> >I'd like to superimpose the maps to in an attempt to find density for a
> >ligand, but I'm having a hard time trying to get this to work. The
> >closest I have come is by superimposing the coordinates for the two
> >forms with lsqkab then using the resulting transformation matrix to skew
> >one of the maps. When I check out the skewed map in coot, it is not
> >quite right (off by around 2 angstrom).
> >
> >Is there another way to do this? I'm guessing some of the tricks used in
> >multi-crystal averaging would be useful here.
> >
> >Thanks in advance for your reply,
> >
> >Andrew Robinson
> >Macquarie University, Australia
> >
> >
> >

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 27 April 2007

Previous message:
Subject: Re: Structures with pseudo-uridine?
From: Poul Nissen pn {- at -} MB {- dot -} AU {- dot -} DK
Date: 2007-04-27

Next message:
Subject: Re: Error with scala after combat
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-04-27