[phenixbb] where to find phenix.phaser 2.2.3 documentation on keywords

Dr G. Bunkoczi gb360 at cam.ac.uk
Wed Mar 24 07:19:40 PDT 2010


Hi Bjørn,

the new keyword syntax is
PACK CUTOFF <num>

and I would also suggest to use PACK SELECT ALLOW This keeps solutions if 
they have less than CUTOFF clashes, as opposed to the current default BEST 
option that will only keep the lowest (if below CUTOFF). This will become 
default at some point.

For completeness, other uses of the keyword: PACK DISTANCE <num> - changes 
the clash distance between Calphas (default 3.0) PACK QUICK ON - performs a 
"quick" packing test by counting only up to ALLOW number of clashes and 
discarding the solution is above.

Please let us know if you have any further queries. There were a lot of 
changes between version 2.1 and 2.2, and we are preparing a wiki for the 
new keyword syntax, which will go online hopefully soon.

BW, Gabor

On Mar 24 2010, Bjørn Panyella Pedersen wrote:

> Dear list I am struggling to find the documentation for Phaser 2.2.3 (as 
> part of phenix.phaser v1.6.289), and more specifically the list of 
> allowed keywords and what their significance is.
>
> In my hands the PACK keyword is no longer allowed in v2.2.3 (works fine 
> in v2.1.4) while two alternatives: SELECT CUTOFF DISTANCE and QUICK are 
> suggested instead. However I cannot find any details on what these do. 
> Ultimately I want to allow packing clashes beyond the default of 10.
>
> A google-search only give me hits on the Phaser homepage with 
> documentation for v.2.1 
> (http://www-structmed.cimr.cam.ac.uk/phaser/documentation/index.html), 
> and the phenix.phaser documentation 
> (http://www.phenix-online.org/documentation/phaser.htm) does not include 
> a keyword-list.
>
>Hope somebody can help with this simple problem.
>
>Best
>Bjørn
>
>

-- 
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     Dr Gabor Bunkoczi

     Cambridge Institute for Medical Research
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