[phenixbb] Selecting ellipsoid of data

Morten Grøftehauge mortengroftehauge at gmail.com
Tue Jul 20 16:18:13 PDT 2010


Kay suggestion is better than mine which would have been
http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/

On 16 July 2010 03:16, Frank von Delft <frank.vondelft at sgc.ox.ac.uk> wrote:

>  Ah.... I was wondering about that:  thanks for the pointer!!
>
>
>
> On 15/07/2010 17:38, Kay Diederichs wrote:
>
> Hi Frank,
>
> "such a tool" is at
> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Aniso_cutoff
>
> where it's meant to be applied to INTEGRATE.HKL which comes out of XDS.
> Doing it this way has the benefit that the statistics printed out by XDS'
> CORRECT (or SCALA/TRUNCATE; there are people who prefer that route) match
> the data you refine agains.
>
> HTH,
>
> Kay
>
> Message: 1
> Date: Thu, 15 Jul 2010 06:32:40 +0100
> From: Frank von Delft<frank.vondelft at sgc.ox.ac.uk><frank.vondelft at sgc.ox.ac.uk>
> To: PHENIX user mailing list<phenixbb at phenix-online.org><phenixbb at phenix-online.org>
> Subject: [phenixbb] Selecting ellipsoid of data
> Message-ID:<4C3E9D78.5030203 at sgc.ox.ac.uk> <4C3E9D78.5030203 at sgc.ox.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi, is there a tool in phenix that allows me to select an ellipsoid of
> data -- specified e.g. by the highest resolutions in three reciprocal
> lattice directions.  (Yes, I'm playing with anisotropy, "playing" being
> the operative word.)
>
> phx
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 14 Jul 2010 22:47:30 -0700
> From: "Ralf W. Grosse-Kunstleve"<rwgk at cci.lbl.gov> <rwgk at cci.lbl.gov>
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Selecting ellipsoid of data
> Message-ID:<201007150547.o6F5lUoL018490 at cci.lbl.gov><201007150547.o6F5lUoL018490 at cci.lbl.gov>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Frank,
>
> Hi, is there a tool in phenix that allows me to select an ellipsoid of
> data -- specified e.g. by the highest resolutions in three reciprocal
> lattice directions.  (Yes, I'm playing with anisotropy, "playing" being
> the operative word.)
>
>
> I'm not aware of such a tool.
>
> Ralf
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 15 Jul 2010 07:15:58 +0100
> From: Frank von Delft<frank.vondelft at sgc.ox.ac.uk><frank.vondelft at sgc.ox.ac.uk>
> To: "Ralf W. Grosse-Kunstleve"<rwgk at cci.lbl.gov> <rwgk at cci.lbl.gov>,
> PHENIX user mailing
>     list<phenixbb at phenix-online.org> <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Selecting ellipsoid of data
> Message-ID:<4C3EA79E.2030503 at sgc.ox.ac.uk> <4C3EA79E.2030503 at sgc.ox.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Ralf
>
> Yeah, I figured.  So if I want to use cctbx, where do I start?  Just a
> pointer to a) package and b) function where I'll see the syntax.
>
> So equation for ellipsoid is x^2/a^2 + y^2/b^2 + z^2/c^2  = 1;  so I
> imagine I take each reflection, convert each of h,k,l to 1/reso, and
> with a = 1/res(a*), I just check whether the above is<  1.
>
> The main thing I still need is to convert h,k,l into orthogonal
> coordinates.... or do I?  I suppose I don't, as what I care for is not
> whether it's "really" an ellipsoid, only whether it cuts through miller
> index space anisotropically.
>
> Hmmmm... I may be able to do it in sftools;  but if you can in<1minute
> give me a link to where to look to get started in cctbx, that would be
> awesome.
>
> (Thanks for listening :)
>
>
>
>
> Hi Frank,
>
>
> Hi, is there a tool in phenix that allows me to select an ellipsoid of
> data -- specified e.g. by the highest resolutions in three reciprocal
> lattice directions.  (Yes, I'm playing with anisotropy, "playing" being
> the operative word.)
>
>  I'm not aware of such a tool.
>
> Ralf
>
>
>
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