Hi, If I may add to that (straight from Garib's mouth) an option that I have not been aware of: adding external keywords (it's in the gui as I discovered. I have not tried it yet).
Adding external keywords: Please have a look the presentation: http://www.ysbl.york.ac.uk/refmac/Presentations/Refmac_Erice_workshop.ppt you need slides 47-50 Cheers, Boaz ----- Original Message ----- From: Ben Eisenbraun <[email protected]> Date: Saturday, October 16, 2010 4:46 Subject: Re: [ccp4bb] update REFMAC To: [email protected] > Hi Ed, > > > To upgrade the Refmac version that I am running from inside > the CCP4i, I > > did the following > > > > mv $CCP4/bin/refmac5 $CCP4/bin/refmac5.5 > > cp refmacgfortran $CCP4/bin/refmac5.6 > > ln -s $CCP4/bin/refmac5.6 $CCP4/bin/refmac5 > > > > It seems to have worked fine. Is there more intelligent > way of doing > > this? > > I asked the same question a few weeks and got a few helpful replies. > > Garib said you can "replace $CBIN/refmac5 with refmac5.6", which > is basically > what you did. Or you can open "ccp4i click "System > administration", select > "configure interface" and jus below "Give full path name for > CCP4 programs > to overcome name conflicts" click "Add a program" There will > appear two > fields. On the right field type refmac5 and on the left field actual > address of the program." > > Liz Potterton suggested that method as well. > > Sabine Schneider pointed out that the monomers dictionary lives at > $CCP4/ccp4-6.1.3/lib/data/monomers/ and is set with the CLIBD_MON > environment variable. Presumably you can just override the > variable to > point to a different directory and ccp4i will do the right thing. > > Boaz Shaanan suggested setting up your Refmac job using the > current task > interface, saving it as a .com file and then editing it by hand > to add the > additional parameters/flags available in Refmac 5.6. > > Finally Peter Cherepanov mentioned that you need the new > fragment library > and noted that version 5.6 uses LINK rather than LINKR. > > Note that I'm just a keyboard puncher, so your mileage may > vary. Thanks to > all for the suggestions. > > -ben > > -- > | Ben > Eisenbraun | Software Sysadmin | > | Structural Biology > Grid | http://sbgrid.org | > | Harvard Medical > School | http://hms.harvard.edu | > Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
