Re: [ccp4bb] anisotropic displacement parameter matrix shelxl

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Help with reducing crystal mosaicity
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-07-09

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Date: 2007-07-10

Subject: Re: anisotropic displacement parameter matrix shelxl
From: "Ralf W {- dot -} Grosse-Kunstleve" rwgk {- at -} YAHOO {- dot -} COM
Date: 2007-07-09

> On the handling of atomic anisotropic displacement
> parameters
> R. W. Grosse-Kunstleve* and P. D. Adams
> J. Appl. Cryst. (2002). 35, 477-480
>
> to look up the above relationship. In the paper it is mentioned that
>
>
Ucart - (lambda)I
=0
>
> is solved using Cardan's formula.

After the paper was published I discovered that my implementation
based on Cardan's formula was numerically unstable in some cases. I
found it too difficult to come up with a fully reliable implementation
and eventually plugged in general eigenvalue code. I've been happy
ever since.

> So I probably oversimplified my solution and have it wrong.

If your goal is to learn more about the eigenvalue problem, this
page is great:

http://en.wikipedia.org/wiki/Eigenvalue

Look for "characteristic polynomial" (that's the equation you quote).

If you just need to find the eigenvalues and vectors, the example
script mentioned in the paper survived almost unchanged:

http://cctbx.svn.sourceforge.net/viewvc/cctbx/trunk/cctbx/cctbx/examples/analyze_adp.py?view=markup

You can install the cctbx in about 30 seconds by using one of the
binary bundles here:

http://cci.lbl.gov/cctbx_build/

Then:

cctbx.python cctbx_sources/cctbx/cctbx/examples/analyze_adp.py

Be sure to reorder the parameters you get from shelx!
Shelx gives you U11 U22 U33 U23 U13 U12, while the cctbx uses
the PDB order U11 U22 U33 U12 U13 U23.

Ralf

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Help with reducing crystal mosaicity
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-07-09

Next message:
Subject: Re: Proper Reference for Phil Evans Program POINTLESS
From: "Winter, G (Graeme)" g {- dot -} winter {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-07-10