Re: [ccp4bb] CCP4i on MacPro under Leopard
Under 10.5.X, sudo doesn't inherit the environment. So the best thing to do is start a root process like this: /bin/bash (or /bin/zsh or /bin/tcsh ) source /usr/local/ccp4-6.0.2/include/ccp4.setup-bash (or whatever it is for your shell) Then issue ccp4i William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Aug 25, 2008, at 6:05 AM, Anita Bentley wrote: My faithful old Mac G5 siezed up and I have to use a brand new MacBook Pro from now on. It's an Intel machine with Leopard. I managed to install CCP4 together with TLK/BLK programmes. After a long while searching for bltwish routines I discovered that they are automatically installed in /usr/local/bin and not in /sw/bin as suggested in the ccp4 setup files (!). With this problem sorted out, I was able to start ccp4i GUI fine. I get the message that I am the first person to run this version ... and should get the right person to configure the interface However, when I try to run ccp4i with sudo in order to have the priviledges to configure it, I am unable to run it: macbookpro-bentley 7% sudo ccp4i /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: /bltwish: No such file or directory /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: exec: /bltwish: cannot execute: No such file or directory I've modified the -sh and -csh files (I have a one-line login.com to get me under csh as user) to no avail. What do I have to do to be able to configure the interface??? The underlying problem is that I cannot run REFMAC in the present state of things, I get the following error: Error from script /usr/local/ccp4-6.0.2/share/ccp4i/scripts/refmac5.script: can't read cell: no such variable which makes me think the configuration of the interface is not quite right. Any help is greatly appreciated! Anita Anita Lewit-Bentley LBPA Ecole Normale Supérieure de Cachan 61, avenue du Président Wilson 94235 Cachan cedex FRANCE tel: 33-(0)1-47 40 76 65 fax: 33-(0)1 47 40 76 71 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] CCP4i on MacPro under Leopard
Thanks a lot for this hint: it works! Including REFMAC, which ran to completion and used Arp/Warp to add waters successfully. Anita Le 25 août 08 à 16:04, William G. Scott a écrit : Under 10.5.X, sudo doesn't inherit the environment. So the best thing to do is start a root process like this: /bin/bash (or /bin/zsh or /bin/tcsh ) source /usr/local/ccp4-6.0.2/include/ccp4.setup-bash (or whatever it is for your shell) Then issue ccp4i William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Aug 25, 2008, at 6:05 AM, Anita Bentley wrote: My faithful old Mac G5 siezed up and I have to use a brand new MacBook Pro from now on. It's an Intel machine with Leopard. I managed to install CCP4 together with TLK/BLK programmes. After a long while searching for bltwish routines I discovered that they are automatically installed in /usr/local/bin and not in /sw/bin as suggested in the ccp4 setup files (!). With this problem sorted out, I was able to start ccp4i GUI fine. I get the message that I am the first person to run this version ... and should get the right person to configure the interface However, when I try to run ccp4i with sudo in order to have the priviledges to configure it, I am unable to run it: macbookpro-bentley 7% sudo ccp4i /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: /bltwish: No such file or directory /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: exec: /bltwish: cannot execute: No such file or directory I've modified the -sh and -csh files (I have a one-line login.com to get me under csh as user) to no avail. What do I have to do to be able to configure the interface??? The underlying problem is that I cannot run REFMAC in the present state of things, I get the following error: Error from script /usr/local/ccp4-6.0.2/share/ccp4i/scripts/refmac5.script: can't read cell: no such variable which makes me think the configuration of the interface is not quite right. Any help is greatly appreciated! Anita Anita Lewit-Bentley LBPA Ecole Normale Supérieure de Cachan 61, avenue du Président Wilson 94235 Cachan cedex FRANCE tel: 33-(0)1-47 40 76 65 fax: 33-(0)1 47 40 76 71 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] CCP4i on MacPro under Leopard
Glad it worked. I should have written sudo /bin/bash or sudo /bin/zsh or sudo /bin/tcsh followed by sourcing the appropriate startup script. However, if I run the tcsh command, I get this error: limit: stacksize: Can't remove limit (Invalid argument) oddly, this does not happen with a non-root version of tcsh. It is easier I think just to use /bin/bash or /bin/zsh in this case. On Aug 25, 2008, at 9:09 AM, Anita Bentley wrote: Thanks a lot for this hint: it works! Including REFMAC, which ran to completion and used Arp/Warp to add waters successfully. Anita Le 25 août 08 à 16:04, William G. Scott a écrit : Under 10.5.X, sudo doesn't inherit the environment. So the best thing to do is start a root process like this: /bin/bash (or /bin/zsh or /bin/tcsh ) source /usr/local/ccp4-6.0.2/include/ccp4.setup-bash (or whatever it is for your shell) Then issue ccp4i William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Aug 25, 2008, at 6:05 AM, Anita Bentley wrote: My faithful old Mac G5 siezed up and I have to use a brand new MacBook Pro from now on. It's an Intel machine with Leopard. I managed to install CCP4 together with TLK/BLK programmes. After a long while searching for bltwish routines I discovered that they are automatically installed in /usr/local/bin and not in /sw/bin as suggested in the ccp4 setup files (!). With this problem sorted out, I was able to start ccp4i GUI fine. I get the message that I am the first person to run this version ... and should get the right person to configure the interface However, when I try to run ccp4i with sudo in order to have the priviledges to configure it, I am unable to run it: macbookpro-bentley 7% sudo ccp4i /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: /bltwish: No such file or directory /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: exec: /bltwish: cannot execute: No such file or directory I've modified the -sh and -csh files (I have a one-line login.com to get me under csh as user) to no avail. What do I have to do to be able to configure the interface??? The underlying problem is that I cannot run REFMAC in the present state of things, I get the following error: Error from script /usr/local/ccp4-6.0.2/share/ccp4i/scripts/refmac5.script: can't read cell: no such variable which makes me think the configuration of the interface is not quite right. Any help is greatly appreciated! Anita Anita Lewit-Bentley LBPA Ecole Normale Supérieure de Cachan 61, avenue du Président Wilson 94235 Cachan cedex FRANCE tel: 33-(0)1-47 40 76 65 fax: 33-(0)1 47 40 76 71 e-mail: [EMAIL PROTECTED]
