where to find phenix.phaser 2.2.3 documentation on keywords
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: [email protected] http://www.bioxray.au.dk
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
-- ################################################## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##################################################
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: [email protected] 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 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
participants (3)
-
Bjørn Panyella Pedersen -
Dr G. Bunkoczi -
Randy Read