[phenixbb] Selecting ellipsoid of data

Kay Diederichs kay.diederichs at uni-konstanz.de
Thu Jul 15 09:38:29 PDT 2010


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>
> To: PHENIX user mailing list<phenixbb at phenix-online.org>
> Subject: [phenixbb] Selecting ellipsoid of data
> Message-ID:<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>
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Selecting ellipsoid of data
> Message-ID:<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>
> To: "Ralf W. Grosse-Kunstleve"<rwgk at cci.lbl.gov>,	PHENIX user mailing
> 	list<phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Selecting ellipsoid of data
> Message-ID:<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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