Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13
Hi folks, Anyone know if this site is temporarily down or is it more permanent? http://bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu Cheers Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry Sent: Tuesday, 9 August 2011 2:28 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13 유상헌 wrote: > Dear all, > > First I’m a beginner of linux and I’m trying to install CCP4 on my 64bit > Fedora 13. > > If there is anyone who successfully installed ccp4 on 64bit fedora13, > > please, instruct me how to install this program in detail. > I recently installed CCP4-6.1.3 from source on fedora 14, 64-bit. After googling solved a few problems it went easily. Maybe the problems are all fixed in 6.2 so try that first. Un-tar the package- read INSTALL (or INSTALL.html or .ps) in the top directory Try to follow the instructions for installing from source and see where you get stuck. Check the list of problems reported and see if there are solutions at http://www.ccp4.ac.uk/problems.php For me, this site had most of the answers: http://bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu For fedora, use "yum install" instead of "apt-get install" and "yum provides" (or whatprovides) instead of "apt-file search" (And unless you are a mac person, you might be more comfortable becoming root rather than prepending every privilege-requiring command with "sudo") If you have trouble with TCL/TK read below-quoted message. Mosflm site has more suggestions. better yet: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/CCP4_on_Fedora_12 Mark Del Campo wrote: > Okay, I got the problem resolved in the following way (thanks go to > Clint > Leysath): > > 1. removed the tcltk++ directory that came with my ccp4 download 2. > installed Activestate's tcltk 8.4.19.2 from > https://www.activestate.com/activetcl/downloads/ > 3. downloaded blt2.4z.tar.gz and the blt2.4z-patch-2 from > http://sourceforge.net/projects/blt/files/ > 4. unpacked blt2.4z.tar.gz and moved the patch file into the blt2.4z > directory 5. patched the blt installation (patch -p1 -i > blt2.4z-patch-2) 6. then reordered statements in blt2.4z/src/bltTree.c > [this is detailed at http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html > under the heading Compilation failure in bltTree on 64-bit machines] > 7. configured the blt install (./configure > --with-tcl=/path/to/ActiveTcl-8.4) > 8. installed blt (make) > 9. for some reason bltwish did not end up in > /path/to/ActiveTcl-8.4/bin even though the configure script said that > is where it would be put, so I moved it to /path/to/ActiveTcl-8.4/bin > 10. edited 1 line in ccp4.setup-bash (setenv CCP4I_TCLTK > /path/to/ActiveTcl-8.4/bin/) > 11. opened a new terminal window& ccp4i works >
Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13
Edward A. Berry wrote: That does look easier, but mainly because you are not installing blt - What do you get for "which bltwish"? presumably in $CCP4I_TCLTK, since ccp4i works. So that means $CCP4_MASTER/tcltk++/bin But how did it get there? maybe from here? ftp://ftp.ccp4.ac.uk/ccp4/6.2.0/extras/
Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13
That does look easier, but mainly because you are not installing blt - What do you get for "which bltwish"? presumably in $CCP4I_TCLTK, since ccp4i works. So that means $CCP4_MASTER/tcltk++/bin But how did it get there? Then your install of activetcltk-8.4 is only for mosflm, which I guess doesn't use bltwish Andreas Förster wrote: Somehow I missed Mark Del Campo's path-towards-a-working-tcltk/blt/wish-email. But does it have to be that complicated? On RHEL 6.1, 64-bit, CCP4 6.2 I do: 1. edit 1 line in ccp4.setup-bash (export CCP4I_TCLTK=$CCP4_MASTER/tcltk++/bin) 2. install Activestate's tcltk 8.5.9.1 from https://www.activestate.com/activetcl/downloads/ 3. go to /path/to/ActiveTcl-8.5/bin and install one additional package: ./teacup install --with-recommends Iwidgets 4. add 1 line to .bashrc (export MOSFLM_WISH=/path/to/ActiveTcl-8.5/bin/wish) 5. open a new terminal: imosflm and ccp4i work (as far as I have tested) Andreas On 09/08/2011 2:46, Edward A. Berry wrote: Edward A. Berry wrote: If you have trouble with TCL/TK read below-quoted message. Mosflm site has more suggestions. better yet: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/CCP4_on_Fedora_12 which says: Now Tcl/Tk tools are bundled with Fedora 12, and they work well for CCP4i/imosflm. Install tcl, tk, blt, itcl, itk, tkimg, tcl-tktreectrl, iwidgets, and tdom packages and set $CCP4I_TCLTK to /usr/bin. BUT the blt bundled with Fedora 14 does not include bltwish. better use patched blt2.4 as described by del Campo below. Apparently same is true of ubuntu and the developers do not consider this a bug, according to the bug report filed by wgscott: https://bugs.launchpad.net/ubuntu/+source/blt/+bug/19148 "not a bug. It doesn't make sense to provide a separate shell for each Tcl Extension. Also, the current blt version is 8.0. just use wish for your scripts: #!/usr/bin/wish package require BLT [...] " I tend to agree with Bill, but if it would be this easy to remove a dependency that makes trouble for newbies like me, maybe CCP4 should do it. Mark Del Campo wrote: Okay, I got the problem resolved in the following way (thanks go to Clint Leysath): 1. removed the tcltk++ directory that came with my ccp4 download 2. installed Activestate's tcltk 8.4.19.2 from https://www.activestate.com/activetcl/downloads/ 3. downloaded blt2.4z.tar.gz and the blt2.4z-patch-2 from http://sourceforge.net/projects/blt/files/ 4. unpacked blt2.4z.tar.gz and moved the patch file into the blt2.4z directory 5. patched the blt installation (patch -p1 -i blt2.4z-patch-2) 6. then reordered statements in blt2.4z/src/bltTree.c [this is detailed at http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html under the heading Compilation failure in bltTree on 64-bit machines] 7. configured the blt install (./configure --with-tcl=/path/to/ActiveTcl-8.4) 8. installed blt (make) 9. for some reason bltwish did not end up in /path/to/ActiveTcl-8.4/bin even though the configure script said that is where it would be put, so I moved it to /path/to/ActiveTcl-8.4/bin 10. edited 1 line in ccp4.setup-bash (setenv CCP4I_TCLTK /path/to/ActiveTcl-8.4/bin/) 11. opened a new terminal window& ccp4i works -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13
Somehow I missed Mark Del Campo's path-towards-a-working-tcltk/blt/wish-email. But does it have to be that complicated? On RHEL 6.1, 64-bit, CCP4 6.2 I do: 1. edit 1 line in ccp4.setup-bash (export CCP4I_TCLTK=$CCP4_MASTER/tcltk++/bin) 2. install Activestate's tcltk 8.5.9.1 from https://www.activestate.com/activetcl/downloads/ 3. go to /path/to/ActiveTcl-8.5/bin and install one additional package: ./teacup install --with-recommends Iwidgets 4. add 1 line to .bashrc (export MOSFLM_WISH=/path/to/ActiveTcl-8.5/bin/wish) 5. open a new terminal: imosflm and ccp4i work (as far as I have tested) Andreas On 09/08/2011 2:46, Edward A. Berry wrote: Edward A. Berry wrote: If you have trouble with TCL/TK read below-quoted message. Mosflm site has more suggestions. better yet: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/CCP4_on_Fedora_12 which says: Now Tcl/Tk tools are bundled with Fedora 12, and they work well for CCP4i/imosflm. Install tcl, tk, blt, itcl, itk, tkimg, tcl-tktreectrl, iwidgets, and tdom packages and set $CCP4I_TCLTK to /usr/bin. BUT the blt bundled with Fedora 14 does not include bltwish. better use patched blt2.4 as described by del Campo below. Apparently same is true of ubuntu and the developers do not consider this a bug, according to the bug report filed by wgscott: https://bugs.launchpad.net/ubuntu/+source/blt/+bug/19148 "not a bug. It doesn't make sense to provide a separate shell for each Tcl Extension. Also, the current blt version is 8.0. just use wish for your scripts: #!/usr/bin/wish package require BLT [...] " I tend to agree with Bill, but if it would be this easy to remove a dependency that makes trouble for newbies like me, maybe CCP4 should do it. Mark Del Campo wrote: Okay, I got the problem resolved in the following way (thanks go to Clint Leysath): 1. removed the tcltk++ directory that came with my ccp4 download 2. installed Activestate's tcltk 8.4.19.2 from https://www.activestate.com/activetcl/downloads/ 3. downloaded blt2.4z.tar.gz and the blt2.4z-patch-2 from http://sourceforge.net/projects/blt/files/ 4. unpacked blt2.4z.tar.gz and moved the patch file into the blt2.4z directory 5. patched the blt installation (patch -p1 -i blt2.4z-patch-2) 6. then reordered statements in blt2.4z/src/bltTree.c [this is detailed at http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html under the heading Compilation failure in bltTree on 64-bit machines] 7. configured the blt install (./configure --with-tcl=/path/to/ActiveTcl-8.4) 8. installed blt (make) 9. for some reason bltwish did not end up in /path/to/ActiveTcl-8.4/bin even though the configure script said that is where it would be put, so I moved it to /path/to/ActiveTcl-8.4/bin 10. edited 1 line in ccp4.setup-bash (setenv CCP4I_TCLTK /path/to/ActiveTcl-8.4/bin/) 11. opened a new terminal window& ccp4i works -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13
Edward A. Berry wrote: If you have trouble with TCL/TK read below-quoted message. Mosflm site has more suggestions. better yet: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/CCP4_on_Fedora_12 which says: Now Tcl/Tk tools are bundled with Fedora 12, and they work well for CCP4i/imosflm. Install tcl, tk, blt, itcl, itk, tkimg, tcl-tktreectrl, iwidgets, and tdom packages and set $CCP4I_TCLTK to /usr/bin. BUT the blt bundled with Fedora 14 does not include bltwish. better use patched blt2.4 as described by del Campo below. Apparently same is true of ubuntu and the developers do not consider this a bug, according to the bug report filed by wgscott: https://bugs.launchpad.net/ubuntu/+source/blt/+bug/19148 "not a bug. It doesn't make sense to provide a separate shell for each Tcl Extension. Also, the current blt version is 8.0. just use wish for your scripts: #!/usr/bin/wish package require BLT [...]" I tend to agree with Bill, but if it would be this easy to remove a dependency that makes trouble for newbies like me, maybe CCP4 should do it. Mark Del Campo wrote: Okay, I got the problem resolved in the following way (thanks go to Clint Leysath): 1. removed the tcltk++ directory that came with my ccp4 download 2. installed Activestate's tcltk 8.4.19.2 from https://www.activestate.com/activetcl/downloads/ 3. downloaded blt2.4z.tar.gz and the blt2.4z-patch-2 from http://sourceforge.net/projects/blt/files/ 4. unpacked blt2.4z.tar.gz and moved the patch file into the blt2.4z directory 5. patched the blt installation (patch -p1 -i blt2.4z-patch-2) 6. then reordered statements in blt2.4z/src/bltTree.c [this is detailed at http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html under the heading Compilation failure in bltTree on 64-bit machines] 7. configured the blt install (./configure --with-tcl=/path/to/ActiveTcl-8.4) 8. installed blt (make) 9. for some reason bltwish did not end up in /path/to/ActiveTcl-8.4/bin even though the configure script said that is where it would be put, so I moved it to /path/to/ActiveTcl-8.4/bin 10. edited 1 line in ccp4.setup-bash (setenv CCP4I_TCLTK /path/to/ActiveTcl-8.4/bin/) 11. opened a new terminal window& ccp4i works
Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13
유상헌 wrote: > Dear all, > > First I’m a beginner of linux and I’m trying to install CCP4 on my 64bit > Fedora 13. > > If there is anyone who successfully installed ccp4 on 64bit fedora13, > > please, instruct me how to install this program in detail. > I recently installed CCP4-6.1.3 from source on fedora 14, 64-bit. After googling solved a few problems it went easily. Maybe the problems are all fixed in 6.2 so try that first. Un-tar the package- read INSTALL (or INSTALL.html or .ps) in the top directory Try to follow the instructions for installing from source and see where you get stuck. Check the list of problems reported and see if there are solutions at http://www.ccp4.ac.uk/problems.php For me, this site had most of the answers: http://bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu For fedora, use "yum install" instead of "apt-get install" and "yum provides" (or whatprovides) instead of "apt-file search" (And unless you are a mac person, you might be more comfortable becoming root rather than prepending every privilege-requiring command with "sudo") If you have trouble with TCL/TK read below-quoted message. Mosflm site has more suggestions. better yet: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/CCP4_on_Fedora_12 Mark Del Campo wrote: > Okay, I got the problem resolved in the following way (thanks go to Clint > Leysath): > > 1. removed the tcltk++ directory that came with my ccp4 download > 2. installed Activestate's tcltk 8.4.19.2 from > https://www.activestate.com/activetcl/downloads/ > 3. downloaded blt2.4z.tar.gz and the blt2.4z-patch-2 from > http://sourceforge.net/projects/blt/files/ > 4. unpacked blt2.4z.tar.gz and moved the patch file into the blt2.4z directory > 5. patched the blt installation (patch -p1 -i blt2.4z-patch-2) > 6. then reordered statements in blt2.4z/src/bltTree.c [this is detailed at > http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html under the heading > Compilation failure in bltTree on 64-bit machines] > 7. configured the blt install (./configure --with-tcl=/path/to/ActiveTcl-8.4) > 8. installed blt (make) > 9. for some reason bltwish did not end up in /path/to/ActiveTcl-8.4/bin even > though the configure script said that is where it would be put, so I moved > it to /path/to/ActiveTcl-8.4/bin > 10. edited 1 line in ccp4.setup-bash (setenv CCP4I_TCLTK > /path/to/ActiveTcl-8.4/bin/) > 11. opened a new terminal window& ccp4i works >
[ccp4bb] Installation of ccp4 on 64bit fedora core 13
Dear all, First I’m a beginner of linux and I’m trying to install CCP4 on my 64bit Fedora 13. If there is anyone who successfully installed ccp4 on 64bit fedora13, please, instruct me how to install this program in detail. I’m very desperate Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture & Life Sciences Seoul National University Seoul 151-921, KOREA
[ccp4bb] Installation of ccp4 on 64bit fedora core 13
Dear all, First I’m a beginner of linux and I’m trying to install CCP4 on my 64bit Fedora 13. If there is anyone who successfully installed ccp4 on 64bit fedora13, please, instruct me how to install this program in detail. I’m very desperate Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture & Life Sciences Seoul National University Seoul 151-921, KOREA
