Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...
Hi Jacob, This is a paper on a large conformational change upon PLP binding. http://www.ncbi.nlm.nih.gov/pubmed/22143761
Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
On Mon, Mar 03, 2014 at 01:16:37PM +0800, wu donghui wrote: gcc version in my Mac OS X 10.8.5 is as below. Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) That's Apple compiler. It supports C and C++ but not Fortran, so you also need a Fortran compiler such as gfortran. checking for gcc... gcc-4.2.1 checking whether the C compiler works... no Did you set CC=gcc-4.2.1? Marcin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
-- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 7:07 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr marcin.woj...@diamond.ac.uk Dear Marcin, Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no But indicating that the C compiler does not work. I will try Fortran compiler shortly and let you know. Best, Donghui On Mon, Mar 3, 2014 at 5:43 PM, Marcin Wojdyr marcin.woj...@diamond.ac.ukwrote: On Mon, Mar 03, 2014 at 01:16:37PM +0800, wu donghui wrote: gcc version in my Mac OS X 10.8.5 is as below. Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) That's Apple compiler. It supports C and C++ but not Fortran, so you also need a Fortran compiler such as gfortran. checking for gcc... gcc-4.2.1 checking whether the C compiler works... no Did you set CC=gcc-4.2.1? Marcin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
Hi If trying to build on Macs (OSX 10.5 - 10.9) I strongly recommend installing either the High Performance Computing gcc/gfortran or investing in the Intel Compilers. http://hpc.sourceforge.net/ http://software.intel.com/en-us/intel-compilers (if you have ) Performance-wise, there's not much to choose between them these days. Clang just doesn't cut the mustard, and rolling your own compilers from the gcc archive can be fraught with difficulty and lead to incorrectly functioning compilers. On 3 Mar 2014, at 11:08, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 7:07 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr marcin.woj...@diamond.ac.uk Dear Marcin, Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works… no But indicating that the C compiler does not work. I will try Fortran compiler shortly and let you know. Best, Donghui On Mon, Mar 3, 2014 at 5:43 PM, Marcin Wojdyr marcin.woj...@diamond.ac.uk wrote: On Mon, Mar 03, 2014 at 01:16:37PM +0800, wu donghui wrote: gcc version in my Mac OS X 10.8.5 is as below. Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) That's Apple compiler. It supports C and C++ but not Fortran, so you also need a Fortran compiler such as gfortran. checking for gcc... gcc-4.2.1 checking whether the C compiler works... no Did you set CC=gcc-4.2.1? Marcin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom 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)
[ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
-- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, did you already take a look into config.log to read the error message why your gcc-compiler does not work? You should start at the end of the log file and scroll backwards until you find the error message. Best, Tim On 03/03/2014 03:51 PM, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin - -- - -- 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/ iD8DBQFTFJl9UxlJ7aRr7hoRAo/PAJwLSzdU2Undrc0tosdeSSpdC1aSxACgvzUP khM2NeDGueN6Saat/3kZ+iU= =Z6Ci -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
Hi I think you must be doing something wrong if you can't run Mosflm from the ccp4 binary install - it runs for me. How are you trying to run it? If you need the compilers to build Mosflm then I *very* strongly recommend using the compilers I mentioned in my earlier e-mail - they are what the developers of Mosflm (i.e. Andrew Leslie and me) use to build the distribution versions. If you don't have them installed, and you need to build the Mosflm executable, then you should certainly install them. On OSX, installing the HPC compilers is a doddle. However, my even stronger recommendation is to use the executables that we build here in Cambridge - they have been built and tested rigorously, and I don't think you will gain anything from building yourself (apart from maybe a headache...). On 3 Mar 2014, at 14:51, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works… no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin 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)
[ccp4bb] Research Associate Position at Imperial College London
A Research Associate position has become available to join the group of Professor Hohenester in the Department of Life Sciences to study the molecular mechanism of laminin polymerisation. For details of the project and to apply online, please visit http://www3.imperial.ac.uk/employment and search for reference NS2014045AB. --- Professor Erhard Hohenester Imperial College London Department of Life Sciences Sir Ernst Chain Building London SW7 2AZ United Kingdom e.hohenes...@imperial.ac.ukmailto:e.hohenes...@imperial.ac.uk +44 (0)20 7594 7701 ---
Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...
Dear Jacob, we published in 2012 the structures of apo and peptide-bound forms of a Dipeptidyl peptidase III: Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6525-30. doi: 10.1073/pnas.1118005109. Epub 2012 Apr 9. http://www.ncbi.nlm.nih.gov/pubmed/22493238 we observed a mainly rotational motion of approximately 60 degrees between the two lobes of the enzyme upon peptide binding. Regards, Gustavo Dr. Gustavo Arruda Bezerra Group Djinovic Department of Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna, Austria http://www.mfpl.ac.at/ Em Quinta-feira, 27 de Fevereiro de 2014 20:43, Keller, Jacob kell...@janelia.hhmi.org escreveu: Dear Crystallographers, Does anyone know of good examples of large, reversible conformational changes occurring between ligand-free and -bound states? Could also be a non-relevant molecule binding, like sulfate or something inducing dubiously -relevant changes. I already know of the calmodulin and periplasmic binding protein families, but does anyone know of others out there? All the best, Jacob Keller *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
BTW, we got one report from a sysadmin who has built ccp4 using Clang (Apple compiler 5.0) + gfortran 4.8 from: http://gcc.gnu.org/wiki/GFortranBinaries#MacOS So it's likely that at least one lab is using CCP4 built with Clang. I'm not aware of any benchmarks, though. Marcin On Mon, Mar 03, 2014 at 12:04:20PM +, Harry Powell wrote: Hi If trying to build on Macs (OSX 10.5 - 10.9) I strongly recommend installing either the High Performance Computing gcc/gfortran or investing in the Intel Compilers. http://hpc.sourceforge.net/ http://software.intel.com/en-us/intel-compilers (if you have ) Performance-wise, there's not much to choose between them these days. Clang just doesn't cut the mustard, and rolling your own compilers from the gcc archive can be fraught with difficulty and lead to incorrectly functioning compilers. On 3 Mar 2014, at 11:08, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 7:07 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr marcin.woj...@diamond.ac.uk Dear Marcin, Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works… no But indicating that the C compiler does not work. I will try Fortran compiler shortly and let you know. Best, Donghui On Mon, Mar 3, 2014 at 5:43 PM, Marcin Wojdyr marcin.woj...@diamond.ac.uk wrote: On Mon, Mar 03, 2014 at 01:16:37PM +0800, wu donghui wrote: gcc version in my Mac OS X 10.8.5 is as below. Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) That's Apple compiler. It supports C and C++ but not Fortran, so you also need a Fortran compiler such as gfortran. checking for gcc... gcc-4.2.1 checking whether the C compiler works... no Did you set CC=gcc-4.2.1? Marcin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom 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) -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] 2 ligands/monomer
Dear all, Does anyone happen to know examples of 2 ligands bind to a single protein / each monomer protein in 2 different ligand binding pockets? I know the following example: (1). phosphofructokinase, which binds ATP as both a ligand and a feedback inhibitor in different sites (2). 2 cAMP bound to each E. coli CAP monomer in the crystal structure. Does any of you know other examples? Thank you so much! Best, Wei
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
Dear Tim, Here I attached the config.log file for your help. I have tried to use either gcc-4.2.1 (Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1), or g++-4.2.1(/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1) or gfortran-4.8.1 compiler. Still same error appeared as attached from the config.log file. Thanks for your attention. Best, Donghui On Mon, Mar 3, 2014 at 11:02 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, did you already take a look into config.log to read the error message why your gcc-compiler does not work? You should start at the end of the log file and scroll backwards until you find the error message. Best, Tim On 03/03/2014 03:51 PM, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin - -- - -- 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/ iD8DBQFTFJl9UxlJ7aRr7hoRAo/PAJwLSzdU2Undrc0tosdeSSpdC1aSxACgvzUP khM2NeDGueN6Saat/3kZ+iU= =Z6Ci -END PGP SIGNATURE- config.log Description: Binary data
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
On Tuesday, 04 March 2014 01:33:58 PM wu donghui wrote: Dear Tim, Here I attached the config.log file for your help. I have tried to use either gcc-4.2.1 (Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1), or g++-4.2.1(/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1) or gfortran-4.8.1 compiler. Still same error appeared as attached from the config.log file. Thanks for your attention. Looks like either you do not have the g++ compiler completely installed, or it's installed some place the configure script doesn't know about. Does it work to compile something using gcc-4.2.1 directly from the command line? If not then you need to get that working first. If it does work, then you need to figure out which of the environmental variables in your interactive session need to be added also to the ccp4 setup script. Note that it's not finding gcc for the C compiles either. It's using the Apple compiler. Ethan Best, Donghui On Mon, Mar 3, 2014 at 11:02 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, did you already take a look into config.log to read the error message why your gcc-compiler does not work? You should start at the end of the log file and scroll backwards until you find the error message. Best, Tim On 03/03/2014 03:51 PM, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin - -- - -- 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/ iD8DBQFTFJl9UxlJ7aRr7hoRAo/PAJwLSzdU2Undrc0tosdeSSpdC1aSxACgvzUP khM2NeDGueN6Saat/3kZ+iU= =Z6Ci -END PGP SIGNATURE-
