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

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

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Subject: Re: Structures with pseudo-uridine?
From: Philippe DUMAS p {- dot -} dumas {- at -} IBMC {- dot -} U-STRASBG {- dot -} FR
Date: 2007-04-27

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

Subject: Re: Superposition of maps from different crystal forms
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-27

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.

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
>
>
>

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

Previous message:
Subject: Re: Structures with pseudo-uridine?
From: Philippe DUMAS p {- dot -} dumas {- at -} IBMC {- dot -} U-STRASBG {- dot -} FR
Date: 2007-04-27

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