Re: [ccp4bb] moleman2 install problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear yamei, my guess is that the download was not completed, or your hard disk is about to break. Try downloading it again. You can also copy files from the command line with the cp command. Best, Tim On 07/24/2014 07:19 AM, Yamei Yu wrote: Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFT0NqrUxlJ7aRr7hoRAugrAJ9wv3WIDOL+1Ti+BBbvuYCnu/JObwCgpmhj W8vdmVM22yJXmF+4vumooFk= =aYck -END PGP SIGNATURE-
Re: [ccp4bb] moleman2 install problem
Hi Tim, I download it again through command line and got another error message:” -bash: /Users/yamei/xutil_osx/osx_moleman2: Bad CPU type in executable It seems the software does match my CPU. The processor of my computer is: 2.3 GHz Intel Core i7 Do you know how to solve this ? Thank you so much! Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn On Jul 24, 2014, at 6:06 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear yamei, my guess is that the download was not completed, or your hard disk is about to break. Try downloading it again. You can also copy files from the command line with the cp command. Best, Tim On 07/24/2014 07:19 AM, Yamei Yu wrote: Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFT0NqrUxlJ7aRr7hoRAugrAJ9wv3WIDOL+1Ti+BBbvuYCnu/JObwCgpmhj W8vdmVM22yJXmF+4vumooFk= =aYck -END PGP SIGNATURE-
Re: [ccp4bb] moleman2 install problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Yamei, I am not sure where the official site for USF is now, but I would use http://xray.bmc.uu.se/usf/ There you can download OSX_binaries for Lion and Snow Leopard. The file in the tar-archive is called 'usf_osx_bin/moleman2' rather than osx_moleman2, therefore I guess to stumbled across an outdated download location. I hope Gerard Kleywegt will correct me if I am wrong. I hope this helps. Tim On 07/24/2014 02:08 PM, Yamei Yu wrote: Hi Tim, I download it again through command line and got another error message:” -bash: /Users/yamei/xutil_osx/osx_moleman2: Bad CPU type in executable It seems the software does match my CPU. The processor of my computer is: 2.3 GHz Intel Core i7 Do you know how to solve this ? Thank you so much! Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn On Jul 24, 2014, at 6:06 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear yamei, my guess is that the download was not completed, or your hard disk is about to break. Try downloading it again. You can also copy files from the command line with the cp command. Best, Tim On 07/24/2014 07:19 AM, Yamei Yu wrote: Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFT0PwpUxlJ7aRr7hoRAi4DAJ0YLbbvfBxV5Nj8cmE+laTJ97ploQCg/C70 5KD2nH0qH/MOyUq89ZPQOG4= =nHJU -END PGP SIGNATURE-
Re: [ccp4bb] moleman2 install problem
Hi Mark Unless you've done something very odd, Snow Leopard binaries should be compatible with Mavericks (and Yosemite, too, when you get to try that). Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 24 Jul 2014, at 13:39, Mark Brooks mark.x.bro...@gmail.com wrote: Hi Yamei, If you're on OS X version 10.9.3, then I guess you're on Mavericks, not Snow Leopard ( https://www.apple.com/uk/osx/ ). Therefore, I guess you will need to download the source code and recompile it, since I don't know that Snow Leopard binaries are compatible with Mavericks. (Probably not, judging from all the re-compiling that I seem to have done recently). (Does anyone know better?) See below for instructions from http://xray.bmc.uu.se/usf/ for recompiling, although under OS X 10.6. Mark ---8- The distribution kit can be found here : Distribution_kit Organisation of the distribution kit 35 programs are available, and each has its own directory with the same name as the program, under the parent directory 'usf'. In the top-level 'usf' directory there is a shell script called 'make_all.csh', and big surprise, if you execute that file it will will build all the programs, leaving executables in both the programs' own subdirectories and also in the collective directory 'usf/bin'. Building under OS X The package has been built under Mac OS X v10.6 using the gfortran compiler. The kit is reported to work under 10.7 Lion, but Xcode 4.1 needs to be installed. Thanks to Jacques-Philippe Colletier for the Lion executables. In order to build yourself you will need to install XCODE which can be downloaded from http://developer.apple.com/technology/xcode.html, and gfortran which can be found here http://www.macresearch.org/gfortran-leopard. You will also find a gfortran dmg file in the distribution. Follow the instructions that come with these installation packages. To be able to download these packages, you will have to register as an Apple Developer. Then type make_all.csh in the downloaded USF directory. On 24 July 2014 06:19, Yamei Yu ymyux...@gmail.com wrote: Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn
Re: [ccp4bb] moleman2 install problem
Hmm. Maybe I'm doing something very wrong, because I get the following when I try those binaries: dyld: Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib Referenced from: /Users/brooks/Downloads/usf_osx_bin/./moleman2 Reason: no suitable image found. Did find: /usr/local/gfortran/lib/libgfortran.3.dylib: mach-o, but wrong architecture Trace/BPT trap: 5 What's that due to? (Stuff seems to break easily nowadays on Macs- perhaps I'm just not as up to speed on libraries, architectures and compilers on Apples as I need to be.) Yamei, I compiled it from source and put a copy here: https://dl.dropboxusercontent.com/u/30290835/bin/moleman2 Download it, then make it executable, run it as follows: chmod a+x ~/Downloads/moleman2 ~/Downloads/moleman2 I hope this helps. Mark P.S. if I run this lipo -info /usr/local/lib/libgfortran.3.dylib it gives: Non-fat file: /usr/local/gfortran/lib/libgfortran.3.dylib is architecture: x86_64 x86_64 is the correct architecture, isn't it? On 24 July 2014 13:45, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote: Hi Mark Unless you've done something very odd, Snow Leopard binaries should be compatible with Mavericks (and Yosemite, too, when you get to try that). Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 24 Jul 2014, at 13:39, Mark Brooks mark.x.bro...@gmail.com wrote: Hi Yamei, If you're on OS X version 10.9.3, then I guess you're on Mavericks, not Snow Leopard ( https://www.apple.com/uk/osx/ ). Therefore, I guess you will need to download the source code and recompile it, since I don't know that Snow Leopard binaries are compatible with Mavericks. (Probably not, judging from all the re-compiling that I seem to have done recently). (Does anyone know better?) See below for instructions from http://xray.bmc.uu.se/usf/ for recompiling, although under OS X 10.6. Mark ---8- The distribution kit can be found here : Distribution_kit http://xray.bmc.uu.se/markh/usf/usf_download.php?file=/markh/usf/usf_distribution_kit.tar.gz Organisation of the distribution kit35 programs are available, and each has its own directory with the same name as the program, under the parent directory 'usf'. In the top-level 'usf' directory there is a shell script called 'make_all.csh', and big surprise, if you execute that file it will will build all the programs, leaving executables in both the programs' own subdirectories and also in the collective directory 'usf/bin'. Building under OS XThe package has been built under Mac OS X v10.6 using the gfortran compiler. The kit is reported to work under 10.7 Lion, but Xcode 4.1 needs to be installed. Thanks to Jacques-Philippe Colletier for the Lion executables. In order to build yourself you will need to install XCODE which can be downloaded from http://developer.apple.com/technology/xcode.html, and gfortran which can be found here http://www.macresearch.org/gfortran-leopard. You will also find a gfortran dmg file in the distribution. Follow the instructions that come with these installation packages. To be able to download these packages, you will have to register as an Apple Developer. Then type make_all.csh in the downloaded USF directory. On 24 July 2014 06:19, Yamei Yu ymyux...@gmail.com wrote: Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn
[ccp4bb] moleman2 install problem
Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn
