Re: [ccp4bb] ccp4i - Directories Project Directory Error
Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] ccp4i - Directories Project Directory Error
William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] ccp4i - Directories Project Directory Error
In both cases, you have to make sure you are setting up the environment appropriately for ccp4, unique to the unix shell you are using. In the case of the ccp4 package you compile with the aid of the fink script, at the start of a shell session, you, or your dot file, needs to issue source /sw/bin/init.sh or source /sw/bin/init.csh for bash and zsh or tcsh, respectively. That in turn sources the appropriate environment setup file in $CCP4/include. On Mar 25, 2008, at 7:47 AM, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] ccp4i - Directories Project Directory Error
Hi Kurt, the CCP4 program package for Mac OS X from the CCP4 download site installs the CCP4 suite under /usr/local or any other path that you provide during installation. There is no such thing as a CCP4.app that can be started by clicking on it. Instead, you have to create in a Terminal.app a .bashrc file in your home directory (/Users/name where name is your user name) and add a line to it that calls the ccp4i setup script, like one of the following lines (check the correct path): source /usr/local/ccp4-6.0.2/bin/ccp4.setup-sh or . /usr/local/ccp4-6.0.2/bin/ccp4.setup-sh After that, this setup script is executed whenever you open a new Terminal.app. You can verify the existence of any CCP4 program by typing, for instance, which fft. The answer should give you the full path of the CCP4 fft program. If you want to use the ccp4i GUI, you should install the tcltkblt.pck for Mac OS X from the CCP4 download site under its default installation path. This is more the UNIX way of installation than the Mac way. I hope that helps, best regards, Dirk. Am 25.03.2008 um 15:47 schrieb Kurt Padilla: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: [EMAIL PROTECTED] ***
Re: [ccp4bb] ccp4i - Directories Project Directory Error
Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] ccp4i - Directories Project Directory Error
I also thought the problem was using the Terminal window and not the X11 window, but, interestingly, typing ccp4i in a Terminal window, not an X11 window does work. X11 does need to be installed and running, -- that could be the problem. (Caveat, this is in 10.4, not 10.5 - I have 10.5 but haven't installed it yet because of the coot discussions) Sue On Mar 25, 2008, at 8:37 AM, Anastassis Perrakis wrote: Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] ccp4i - Directories Project Directory Error
Sue, Currently, when I type in ccp4i into Terminal, X11 launches and then CCP4 does too. I am running OS X 10.5 with a fink installation. Kurt On Tue, Mar 25, 2008 at 12:04 PM, Sue Roberts [EMAIL PROTECTED] wrote: I also thought the problem was using the Terminal window and not the X11 window, but, interestingly, typing ccp4i in a Terminal window, not an X11 window does work. X11 does need to be installed and running, -- that could be the problem. (Caveat, this is in 10.4, not 10.5 - I have 10.5 but haven't installed it yet because of the coot discussions) Sue On Mar 25, 2008, at 8:37 AM, Anastassis Perrakis wrote: Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] ccp4i - Directories Project Directory Error
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 This is a 10.5 feature : when an application tries to connect to the X11 window server, X11 is automatically launched (unless it was already running). Hence in Leopard you can call ccp4i from within Terminal.app without much more to setup than the regualr CCP4 setup. Serge. Le 25 mars 08 à 17:32, Kurt Padilla a écrit : Sue, Currently, when I type in ccp4i into Terminal, X11 launches and then CCP4 does too. I am running OS X 10.5 with a fink installation. Kurt On Tue, Mar 25, 2008 at 12:04 PM, Sue Roberts [EMAIL PROTECTED] wrote: I also thought the problem was using the Terminal window and not the X11 window, but, interestingly, typing ccp4i in a Terminal window, not an X11 window does work. X11 does need to be installed and running, -- that could be the problem. (Caveat, this is in 10.4, not 10.5 - I have 10.5 but haven't installed it yet because of the coot discussions) Sue On Mar 25, 2008, at 8:37 AM, Anastassis Perrakis wrote: Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED] -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkfpLPAACgkQlz6UVQtc2uwjGgCeK+8Fb6esGzt4Qcjcv13mKeyS ZewAmgN/vIIkKY77YTTdEr3Yv3a2sC05 =Kf12 -END PGP SIGNATURE-
Re: [ccp4bb] ccp4i - Directories Project Directory Error
That is exactly how it is supposed to work with 10.5. No need to use an xterm, and it sets the DISPLAY variable automatically. I assume you have write-permissions in the directory it is trying to make the .CCP4 directory? On Mar 25, 2008, at 9:32 AM, Kurt Padilla wrote: Sue, Currently, when I type in ccp4i into Terminal, X11 launches and then CCP4 does too. I am running OS X 10.5 with a fink installation. Kurt On Tue, Mar 25, 2008 at 12:04 PM, Sue Roberts [EMAIL PROTECTED] wrote: I also thought the problem was using the Terminal window and not the X11 window, but, interestingly, typing ccp4i in a Terminal window, not an X11 window does work. X11 does need to be installed and running, -- that could be the problem. (Caveat, this is in 10.4, not 10.5 - I have 10.5 but haven't installed it yet because of the coot discussions) Sue On Mar 25, 2008, at 8:37 AM, Anastassis Perrakis wrote: Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
[ccp4bb] ccp4i - Directories Project Directory Error
Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] ccp4i - Directories Project Directory Error
If I move my .CCP4 directory out of the way and start ccp4i, it makes a new one: zsh-% ccp4i 22:14:16 Creating a home directory for CCP4 at /Users/wgscott/.CCP4 22:14:16 Creating CCP4i shadow area at /Users/wgscott/.CCP4/CCP4I_TOP 22:14:16 Creating shadow subdirectory /Users/wgscott/.CCP4/CCP4I_TOP/bin 22:14:16 Creating shadow subdirectory /Users/wgscott/.CCP4/CCP4I_TOP/src 22:14:16 Creating shadow subdirectory /Users/wgscott/.CCP4/CCP4I_TOP/etc Are you sure it isn't there? What do you get for ls ~/.CCP4 By the way the unix command for making a directory like this is mkdir ~/.CCP4 but the GUI appears to do that automatically. Maybe you are trying to make the thing with the Finder (Apple's file browser)? Best to avoid it for anything unixy. It is a carbon-based relic of pre-osx days. On Mar 21, 2008, at 9:34 PM, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
