Dear Roger, The Phaser developers contribute Phaser to both CCP4 and Phenix, so it's better to contact us directly rather than, say, going through the phenix help, especially if it's a CCP4 specific issue.
The syntax of the call to HySS in the Phaser SAD phasing pipeline hasn't changed for at least two years and it used to work, so someone working on HySS must recently have tidied up the syntax (which could be more consistent throughout Phenix in the use of hyphens and underscores), without realising that it would break the SAD phasing pipeline in ccp4i. The documentation on the Phenix website is actually inconsistent on this point, with one page (http://www.phenix-online.org/download/documentation/cci_apps/hyss/examples.html) still giving the syntax with hyphens. We'll fix the syntax of the HySS call for the next CCP4 update. In the meantime, you can choose the SHELXC/D option to find sites or run HySS separately and provide the substructure PDB file to the pipeline. Thanks for reporting the problem! Best wishes, Randy Read On 29 Jan 2014, at 17:33, Roger Rowlett <[email protected]> wrote: > Is there a scripting error in > ccp4-6.4.0/share/ccp4i/scripts/phaser_EP.script? CCP4i jobs fail with an > argument format error, e.g., > > Error interpreting command line argument as a parameter definition: > "data-label=F_whatever(+)" > Improper definition name "data-label" > > I think phenix requires underscores, not hyphens, e.g. "data_label", > "pdb_only" etc. Even the phenix documentation page is conflicted, showing > both "data-label" and "data_label". Maybe is isn't supposed to matter, but in > Phenix 1.8.4, it apparently does matter. > > Is this something that could be fixed in the next CCP4 update? Or should I > direct this to the phenix developers? > > Cheers, > > _______________________________________ > Roger S. Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: [email protected] ------ 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
