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

Randy Read rjr27 at cam.ac.uk
Wed Mar 24 07:24:25 PDT 2010

Dear Bjorn,

Sorry for the trouble!  We made a decision some time ago to switch from old-fashioned web pages to a Wiki format (which is easier for us to update wherever we are), and all the new documentation is on the Wiki.  We've delayed announcing it because we keep thinking that we should spend a few days going through it thoroughly first.

But if it's causing trouble to users, then perhaps it's better to make the URL public knowledge.  We've been using the documentation internally for a while, so it's probably mostly fine -- but please send feedback if you find any errors!

The URL is: http://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software

Note that by using a Wiki format we've been able to add a new feature, a "User Stories" page where people can describe a strategy they used to overcome a difficult problem.  We've put in a couple of examples and hope to expand this, but if you want to add one, you just have to create an account and it should be reasonably straightforward.

All the best,

Randy Read

On 24 Mar 2010, at 13:38, 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
> -- 
> Bjørn Panyella Pedersen, PhD
> Postdoc
> PUMPKIN, Centre for Membrane Pumps in Cells and Disease
> University of Aarhus, Dept. Molecular Biology
> Gustav Wieds Vej 10C DK-8000 Aarhus C, Denmark
> Phone: +45 89425261
> E-mail: bjopp at bioxray.au.dk
> http://www.bioxray.au.dk
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
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