Re: [ccp4bb] configuration or install issue with tk
Edward's suggestion worked.� Coot doesn't work, several library and module error messages, but I'm going to try to get 0.6 running anyway, since the current CCP4 still includes the older 0.5.2.� Thanks to everyone for their feedback. Stuart On Mon 12/14/09 11:27 PM , "Edward A. Berry" wrote: Mark A. White wrote: > Stuart, > > Are you logged-in as root or are you working in a root shell ( using su > or sudo)? Depending on your security settings X-windows may not permit a > program that is run from a root shell to access the display, which > belongs to the user logged-in through X-windows. Another way around this (assuming you have ssh server running) is login to a graphics desktop as yourself, then "ssh r...@localhost" Depending how your SSH, SSHD are configured, you may have to ssh -X or ssh -Y, but the X11 server will be available to the "remote" session so you can run ccp4i (or nedit or xclock or whatever X application), with copy and paste between the remote session window(s) and local, all without having to violate the taboo of never starting X as root. > > I get around the administrator access issue by installing CCP4, and all > other non-OS software, with non-root ownership, a non-root administrator > account, which shares the environment with all other users. This is also great for setting up crystallography for a number of workstations- install all the programs as a normal user on an nfs-mounted disk. Now whoever mounts that disk can source your master setup file and run the programs. Rather than installing as root in the usual /usr/local/bin/ or wherever, on every workstation. The actual system disks then just contain the operating system, which you can reinstall in a few hours (or less from an image) if they become corrupted or need to be updated to the latest distro. Stuart Endo-Streeter wrote: > I was running from a root shell. Ubuntu does not let me login as root. That is normally a good thing, but if I remember correctly to finish the ccp4i setup last time I on a CentOS system I had to login as root. I will try to reinstall tomorrow using sudo, but frankly I hate using it. > I don't think you need to reinstall- just open a terminal in your graphics desktop, ssh -X r...@localhost, verify that $DISPLAY is set and "xclock" works, then source ccp4.setup and run ccp4i. (could be wrong about that, though) Ed
Re: [ccp4bb] configuration or install issue with tk
On Mon, 14 Dec 2009, Edward A. Berry wrote: Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. Another way around this (assuming you have ssh server running) is login to a graphics desktop as yourself, then "ssh r...@localhost" Depending how your SSH, SSHD are configured, you may have to ssh -X or ssh -Y, but the X11 server will be available to the "remote" session so you can run ccp4i (or nedit or xclock or whatever X application), with copy and paste between the remote session window(s) and local, all without having to violate the taboo of never starting X as root. You have to ensure that X11Forwarding is set to 'yes' in /etc/ssh/sshd_config.
Re: [ccp4bb] configuration or install issue with tk
Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. Another way around this (assuming you have ssh server running) is login to a graphics desktop as yourself, then "ssh r...@localhost" Depending how your SSH, SSHD are configured, you may have to ssh -X or ssh -Y, but the X11 server will be available to the "remote" session so you can run ccp4i (or nedit or xclock or whatever X application), with copy and paste between the remote session window(s) and local, all without having to violate the taboo of never starting X as root. I get around the administrator access issue by installing CCP4, and all other non-OS software, with non-root ownership, a non-root administrator account, which shares the environment with all other users. This is also great for setting up crystallography for a number of workstations- install all the programs as a normal user on an nfs-mounted disk. Now whoever mounts that disk can source your master setup file and run the programs. Rather than installing as root in the usual /usr/local/bin/ or wherever, on every workstation. The actual system disks then just contain the operating system, which you can reinstall in a few hours (or less from an image) if they become corrupted or need to be updated to the latest distro. Stuart Endo-Streeter wrote: I was running from a root shell. Ubuntu does not let me login as root. That is normally a good thing, but if I remember correctly to finish the ccp4i setup last time I on a CentOS system I had to login as root. I will try to reinstall tomorrow using sudo, but frankly I hate using it. I don't think you need to reinstall- just open a terminal in your graphics desktop, ssh -X r...@localhost, verify that $DISPLAY is set and "xclock" works, then source ccp4.setup and run ccp4i. (could be wrong about that, though) Ed
Re: [ccp4bb] configuration or install issue with tk
I was running from a root shell. Ubuntu does not let me login as root. That is normally a good thing, but if I remember correctly to finish the ccp4i setup last time I on a CentOS system I had to login as root. I will try to reinstall tomorrow using sudo, but frankly I hate using it. Stuart -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene Sent: Monday, December 14, 2009 21:07 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] configuration or install issue with tk With 'sudo' you should not have this issue. I agree, though, that having a separate user account to install crystallographic programs is quite an advantage from an administrative point of view. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 14 Dec 2009, Mark A. White wrote: > Stuart, > > Are you logged-in as root or are you working in a root shell ( using su > or sudo)? Depending on your security settings X-windows may not permit a > program that is run from a root shell to access the display, which > belongs to the user logged-in through X-windows. > > I get around the administrator access issue by installing CCP4, and all > other non-OS software, with non-root ownership, a non-root administrator > account, which shares the environment with all other users. For one > thing, I do not want to source the multitude of /etc/csh.cshrc and > .bashrc files as root. I am sure that others have different, and > probably more elegant, solutions to this problem. > > PS. It also seems that the TCL/TK environment is not set in the root > shell you are using. > > Good luck, > Mark > > > On Mon, 2009-12-14 at 16:51 -0600, Stuart Endostreeter wrote: > Fellow users, > > I just installed v6.1.2 on Ubuntu 9.0.4 today and have run > into the following problem when I try to run ccp4i for the > first time as root to configure the program: > > r...@:/home//Documents# ccp4i > No protocol specified > Application initialization failed: couldn't connect to > display ":0.0" > Error in startup script: can't read "tk_version": no such > variable > while executing > "catch "set system(TK_VERSION) $tk_version"" > (file "/usr/local/ccp4/ccp4-6.1.2/ccp4i/bin/ccp4i.tcl" > line 1) > (file "/usr/local/ccp4/ccp4-6.1.2//bin/ccp4i" line 1) > > The odd thing is that I can launch ccp4i just fine as a > regular user, but then of course I get the message about the > first time ccp4i has been run and the need to configure it, > which requires administrator level access. > > > Anyone have any ideas? > > > Thanks, > Stuart Endo-Streeter > > Yours sincerely, > > Mark A. White, Ph.D. > Assistant Professor, Dept. Biochemistry and Molecular Biology, > Manager, Sealy Center for Structural Biology and Molecular Biophysics > X-ray Crystallography Laboratory, > Basic Science Building, Room 6.660 C > University of Texas Medical Branch > Galveston, TX 77555-0647 > Tel. (409) 747-4747 > Cell. (409) 539-9138 > Fax. (409) 747-4745 > mailto://wh...@xray.utmb.edu > http://xray.utmb.edu > http://xray.utmb.edu/~white >
Re: [ccp4bb] configuration or install issue with tk
With 'sudo' you should not have this issue. I agree, though, that having a separate user account to install crystallographic programs is quite an advantage from an administrative point of view. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 14 Dec 2009, Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. I get around the administrator access issue by installing CCP4, and all other non-OS software, with non-root ownership, a non-root administrator account, which shares the environment with all other users. For one thing, I do not want to source the multitude of /etc/csh.cshrc and .bashrc files as root. I am sure that others have different, and probably more elegant, solutions to this problem. PS. It also seems that the TCL/TK environment is not set in the root shell you are using. Good luck, Mark On Mon, 2009-12-14 at 16:51 -0600, Stuart Endostreeter wrote: Fellow users, I just installed v6.1.2 on Ubuntu 9.0.4 today and have run into the following problem when I try to run ccp4i for the first time as root to configure the program: r...@:/home//Documents# ccp4i No protocol specified Application initialization failed: couldn't connect to display ":0.0" Error in startup script: can't read "tk_version": no such variable while executing "catch "set system(TK_VERSION) $tk_version"" (file "/usr/local/ccp4/ccp4-6.1.2/ccp4i/bin/ccp4i.tcl" line 1) (file "/usr/local/ccp4/ccp4-6.1.2//bin/ccp4i" line 1) The odd thing is that I can launch ccp4i just fine as a regular user, but then of course I get the message about the first time ccp4i has been run and the need to configure it, which requires administrator level access. Anyone have any ideas? Thanks, Stuart Endo-Streeter Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
Re: [ccp4bb] configuration or install issue with tk
Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. I get around the administrator access issue by installing CCP4, and all other non-OS software, with non-root ownership, a non-root administrator account, which shares the environment with all other users. For one thing, I do not want to source the multitude of /etc/csh.cshrc and .bashrc files as root. I am sure that others have different, and probably more elegant, solutions to this problem. PS. It also seems that the TCL/TK environment is not set in the root shell you are using. Good luck, Mark On Mon, 2009-12-14 at 16:51 -0600, Stuart Endostreeter wrote: > Fellow users, > > I just installed v6.1.2 on Ubuntu 9.0.4 today and have run into the > following problem when I try to run ccp4i for the first time as root > to configure the program: > > r...@:/home//Documents# ccp4i > No protocol specified > Application initialization failed: couldn't connect to display ":0.0" > Error in startup script: can't read "tk_version": no such variable > while executing > "catch "set system(TK_VERSION) $tk_version"" > (file "/usr/local/ccp4/ccp4-6.1.2/ccp4i/bin/ccp4i.tcl" line 1) > (file "/usr/local/ccp4/ccp4-6.1.2//bin/ccp4i" line 1) > > The odd thing is that I can launch ccp4i just fine as a regular user, > but then of course I get the message about the first time ccp4i has > been run and the need to configure it, which requires administrator > level access. > > > Anyone have any ideas? > > > Thanks, > Stuart Endo-Streeter Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
[ccp4bb] configuration or install issue with tk
Fellow users, I just installed v6.1.2 on Ubuntu 9.0.4 today and have run into the following problem when I try to run ccp4i for the first time as root to configure the program: r...@:/home//Documents# ccp4i No protocol specified Application initialization failed: couldn't connect to display ":0.0" Error in startup script: can't read "tk_version": no such variable ��� while executing "catch "set system(TK_VERSION) $tk_version"" ��� (file "/usr/local/ccp4/ccp4-6.1.2/ccp4i/bin/ccp4i.tcl" line 1) ��� (file "/usr/local/ccp4/ccp4-6.1.2//bin/ccp4i" line 1) The odd thing is that I can launch ccp4i just fine as a regular user, but then of course I get the message about the first time ccp4i has been run and the need to configure it, which requires administrator level access. Anyone have any ideas? Thanks, Stuart Endo-Streeter
