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Yes, that is a general "problem" with sudo, with the latest version distributed in OS X. Briefly, sudo (and I have noticed other programs, like screen) don't inherit the environment, so sudo ccp4i no longer works. sudo -s spawns a root shell. Then you can source the environment file, and then it will all work. This PITA is supposedly a security enhancement. (Big Brother knows what is best for you.) On Fri, April 25, 2008 2:57 pm, Patrick Loll wrote: > 1. I was sourcing /sw/bin/init.csh, so that wasn't the problem...but: > > 2. I did find the problem (at least for the precompiled version from > UC Santa Cruz): For some reason "sudo ccp4i" gave the error message, > but just "ccp4i" (without the sudo) worked OK. (Although I thought > the first time you launched ccp4i you were supposed to do it using > sudo...??). Anyway, I'm good (although peeved at my continuing > inability to master sudo. I miss living on the edge with root). > > 3. I didn't try to debug the binaries I got from the ccp4 site, since > I now have a working package. However, Iain Kerr kindly provided > this info, which may prove useful to other small brains out there: > >> ccp4.setup is in ccp4-6.0.2/bin...it used to be in include..is that >> your problem ? >> >> Also, there's no ccp4i folder....the ccp4i binary is in bin/ also. > > > Note to the long-suffering folks at the secret underground world > headquarters of ccp4: Small brain or no, I spent a lot of time > looking around for some clue as to how to complete the install for > the ccp4 package, to no avail; a README file to accompany the > installer would not be unwelcome... > > Thanks, > > Pat > > > On 25 Apr 2008, at 4:56 PM, William Scott wrote: > >> You need to run >> >> source /sw/bin/init.sh >> >> if you use bash or zsh >> >> or >> >> source /sw/bin/init.csh >> >> if you use tcsh. >> >> this will automatically set up the environment variables and then >> it will do what you want it to (which is to set up the ccp4 >> environment according to whichever shell you might be using). >> >> >> On Apr 25, 2008, at 1:19 PM, Patrick Loll wrote: >> >>> Accck! >>> >>> 1. I tried to install Bill Scott's precompiled ccp4 on an intel >>> mac running OS X 10.5. When attempting launch ccp4i, I receive >>> this error message: >>> >>> /sw/share/xtal/ccp4-6.0.2/ccp4i/bin/ccp4i: line 4 /bltwish: no >>> such file or directory >>> >>> Typing "which bltwish" returns /sw/bin/bltwish, which jibes with >>> the definition of $CCP4I_TCLTK, so I'm not sure where the problem >>> is... >>> >>> 2. Pfui. So next I tried jettisoning the apt-get installation, >>> and instead used the installer downloaded from the ccp4 site >>> (ccp4-6.0.2-osx-i386.dmg.gz). This goes swimmingly, until I >>> actually try to do something. Commands like "ccp4i" or "mtzdump" >>> aren't recognized, so I go looking for the ccp4.setup file; but >>> it's not there. Huh? Also, there's no folder named ccp4i, even >>> though this install is supposed to include it... >>> >>> It's Friday, and I'm at the nadir of my weekly brain function, so >>> perhaps some kind soul will tell me where I'm going astray. >>> >>> Thanks, >>> >>> Pat >>> >>> --------------------------------------------------------------------- >>> ------------------ >>> Patrick J. Loll, Ph. D. >>> Professor of Biochemistry & Molecular Biology >>> Director, Biochemistry Graduate Program >>> Drexel University College of Medicine >>> Room 10-102 New College Building >>> 245 N. 15th St., Mailstop 497 >>> Philadelphia, PA 19102-1192 USA >>> >>> (215) 762-7706 >>> [log in to unmask] >>> > > ------------------------------------------------------------------------ > --------------- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Director, Biochemistry Graduate Program > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > [log in to unmask] > > William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/