Re: [ccp4bb] SHELX-2013 release and homepage
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 phew - and people claim, macs were user-friendly. On Linux you just add '-static' (at least for command line tools as the shelx programs) and make the sane assumption that the kernel is less than say 10 years old... Tim On 02/26/2013 04:50 PM, Guangyu Zhu wrote: I just downloaded it. I'm using Mac 10.5.8 and getting error messages: dyld: unknown required load command 0x8022 Trace/BPT trap Google search shows that: You should contact the developer of this application. Only the developer can fix this. The application was incorrectly built on a OS X 10.6 machine for a OS X 10.5 machine. The developer can fix this by considering three things: 1. Using the correct compiler parameters: gcc-4.2 -mmacosx-version-min=10.5 -isysroot /Developer/SDKs/MacOSX10.5.sdk ... 2. Using the correct linker settings (setting environment variable before link command). This is required, so that the OS X 10.6 linker will not use the loader command 'LC_DYLD_INFO_ONLY' (=0x8022), because OS X 10.5 does not understand this command: export MACOSX_DEPLOYMENT_TARGET=10.5 (or setenv MACOSX_DEPLOYMENT_TARGET=10.5) After this is fixed, one can check if the application was correctly built for OS X 10.5 by running 'otool': otool -l binary The correct binary should not contain any 'LC_DYLD_INFO_ONLY' load commands (only 'LC_DYLD_INFO' commands). (also see my blog article http://grauonline.de/wordpress/?p=71 ) Is it possible to build one for Mac 10.5.8? Thanks! Guangyu Zhu On 2/26/13 3:32 AM, George Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: As some of you have already discovered, there is a major new release of the whole of SHELX (the first since 1997) complete with a new homepage that should make downloads easier. To obtain the programs, please point your browser to: http://shelx.uni-ac.gwdg.de/SHELX/ and then 'register' (top of blue menu, upper left). You will then receive the password immediately by email and can then go to 'downloads'. The procedure has been designed to make life difficult for spammers etc. A little program (in FORTRAN of course) turns the registrations into a sorted users' list, which I hand-edit where necessary before it appears on the homepage, this may take a few days. The homepage also provides access to extensive documentation, FAQs etc. Please let me know of any problems (even typos) with the homepage and programs, with so much new material there are sure to be some bugs. The new versions replace all previous versions including beta-tests and almost all the programs have been improved since their last beta-test version (see 'recent changes'). In particular, the new shelxe_2013/2 corrects a couple of serious bugs in the autotracing from MR models and MRSAD present in the beta-test 2013/1. George -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 - -- - -- 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 Mozilla - http://enigmail.mozdev.org/ iD8DBQFRLduMUxlJ7aRr7hoRAkNUAJ99nANlYCXYmlOqTpvKnDJyg+A1bwCdF7GA Ag8n9o/IzBAkuX+HBfH8cMw= =WBV3 -END PGP SIGNATURE-
[ccp4bb] Early Bird Deadline 1st March! 11th International Conference on Biological Synchrotron Radiation (BSR), Hamburg, Germany, 8-11 Sept 2013
*Early bird registration deadline Friday 1st March 2013!* *REGISTER NOW!!!* *11th International Conference on Biological Synchrotron Radiation (BSR)* *Hamburg, Germany* *8th - 11th September 2013* The conference aims to bring together scientists involved in the methodical developments on synchrotron and laser sources with a broad community of biologists with an ambition to make the best use of the most advanced infrastructures in structural biology. Topics include: Biological small angle X-ray scattering Macromolecular X-ray crystallography Biological X-ray imaging and spectroscopy Biological sample preparation Free electron laser applications Synchrotron instrumentation Industrial applications Structural biology hybrid methods Ultimate storage rings For more information and to register, please go to: www.bsr2013.org http://www.bsr2013.org Looking forward to seeing you in Hamburg! Matthias Wilmanns, Dmitri Svergun (EMBL Hamburg) -- Dr. Rosemary Wilson Scientific Training and Public Relations Officer EMBL c/o DESY Notkestrasse 85, Building 25a 22603 Hamburg Germany Tel: 0049 (0)40 89902 228 Fax: 0049 (0)40 89902 149 Email:r.wil...@embl-hamburg.de www.embl-hamburg.de
[ccp4bb] compiling refmac5 on Ubuntu 12.04
I am trying to compile refmac from source on a machine running Ubuntu 12.04. In a nutshell, after some troubleshooting I end up with executable that generates a segmentation fault. Log-file states that CCP4 library signal ccp4_parser:Failed to open external command file (Success) raised in ccp4_parser (hardly a success). Potentially relevant details are that I had to compile libccp4 and libmmdb to get to this point. If I don't configure the CCP4, I get this when trying to run refmac CCP4 library signal ccp4_general:Cannot open environ.def (Error) raised in ccp4fyp refmacgfortran: Cannot open environ.def refmacgfortran: Cannot open environ.def So perhaps it's some incompatibility between libccp4/libmmdb that I compiled and those that came with CCP4 installation (by the way, the new update feature rocks indeed). But I tried lifting these libraries from CCP4 installation when compiling refmac and I get the same segmentation fault. Any suggestions for troubleshooting/advice on how to compile refmac from source are appreciated. Refmac version is 5.7.0032. Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] Postdoc Position in Structural Biology of Membrane Proteins
Postdoc Position in Structural Biology of Membrane Proteins A postdoc position is immediately available at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, to study the mechanism of membrane transporters using X-ray crystallography in combination with various biochemical techniques (http://saturn.med.nyu.edu/research/sb/wanglab/). The Skirball Institute is located in the middle of Manhattan. Strong background in cell culture, eukaryotic protein expression, membrane protein biochemistry, or structural biology is required. Send CV, statement of research interest and names of three references to Da-Neng Wang at w...@saturn.med.nyu.edu. Da-Neng Wang, Ph.D. Professor Structural Biology Program Skirball Institute of Biomolecular Medicine New York University School of Medicine 540 First Avenue New York, NY 10016 USA Phone: (212) 263-8634 Fax: (212) 263-8951 E-mail:w...@saturn.med.nyu.edu Web:http://saturn.med.nyu.edu/research/sb/wanglab/ -
Re: [ccp4bb] Additives to bacterial cultures to improve solubility
Side note, Has anyone tried this in a non-E. coli expression system? Thanks, Lori Lori Horton, Ph.D. Koehler Lab lori.b.hor...@uth.tmc.edumailto:lori.b.hor...@uth.tmc.edumailto:lori.b.hor...@uth.tmc.edu 713-500-5451 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of A K [alek6...@gmail.com] Sent: Tuesday, February 26, 2013 4:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Additives to bacterial cultures to improve solubility Mark, you can try low percentage of ethanol as well, as it increases the expression of some chaperones (can't find the paper right now!). Alex On Tue, Feb 26, 2013 at 2:08 AM, Mark J van Raaij mjvanra...@cnb.csic.esmailto:mjvanra...@cnb.csic.es wrote: Dear All, We are considering trying additives to bacterial cultures to see if they improve solubility of some proteins we express: L-arginine, glycyl-glycine, sorbitol and betaine. I would be glad to receive recommendations and experiences, also if they haven't worked. Side-question: should we get cell culture-certified compounds, or would normal, much more economical ones suffice? (i.e. are they likely to contain side-products that would affect bacterial growth?). Greetings, Mark Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616tel:%28%2B34%29%2091%20585%204616 http://www.cnb.csic.es/~mjvanraaijhttp://www.cnb.csic.es/%7Emjvanraaij -- David J. Leibly Graduate Student, Yeates Lab Dept. Chem Biochem Univ. of California, Los Angeles Boyer Hall 269B (310) 825-8901
[ccp4bb] Cell free expression
Dear all Out of curiosity, are cell free expression systems using E. coli or insect cell extracts useful for membrane protein expression-crystallization? What are the costs associated with these systems? Thank you. Theresa
Re: [ccp4bb] Cell free expression
I've just read that today (even if it is NMR). http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2033.html /E. coli/ or insects cells are so easy to grow that you should be able to do your own cell extrats easily. Xavier Le 27/02/2013 19:25, Theresa Hsu a écrit : Dear all Out of curiosity, are cell free expression systems using E. coli or insect cell extracts useful for membrane protein expression-crystallization? What are the costs associated with these systems? Thank you. Theresa
[ccp4bb] Postdoc Position
Applications are invited for a postdoctoral position in the Washington University at St. Louis. The NIH supported research will focus on the structure and function of intramembrane enzymes. Studies will use multidisciplinary approaches including macromolecular X-ray crystallography, biochemistry, membrane biology, and cell biology. Salary commensurates with experience. Applicants should send their CV with contact information of references to l...@biochem.wustl.edu.
[ccp4bb] Protein Production Core Director - Job Opening - U or Oklahoma
Posted on behalf of Ann West: Job Opening for Protein Production Core Facility Director. The Department of Chemistry and Biochemistry (http://chem.ou.edu) at the University of Oklahoma, Norman Campus (http://www.ou.edu) invites applications for a full-time staff position as Director of the Protein Production Core (PPC) as part of the NIH-sponsored Oklahoma Center of Biomedical Research Excellence (CoBRE) in Structural Biology (http://structuralbiology.ou.edu). We seek an individual with a Ph.D. degree in Chemistry, Biochemistry, or Physics (or a related relevant field) OR a combination of education and experience (e.g. M.S. degree plus equivalent job-related experience). The successful applicant is expected to: (i) direct and oversee the operation, maintenance and administration of the PPC, (ii) spearhead the establishment and management of the PPC, and (iii) engage OU researchers as well as external researchers in collaborative research projects. Duties include but are not limited to the purchase, installation, testing/calibration, operation and maintenance of sophisticated equipment associated with protein expression and purification, the training and supervision of users, and assisting users in preparation of grant proposals, research papers and progress reports. An essential aspect of the job will entail development of a business plan to sustain the core facility. The core director is expected to partner with and provide expert advice to researchers wishing to express and purify recombinant proteins from bacteria, yeast, insect and/or mammalian cell culture. Previous training and experience in molecular biology, cell culture and protein purification techniques (e.g. FPLC, HPLC) are required. The successful candidate must have excellent interpersonal, communication and organizational skills. A competitive salary will be offered, commensurate with experience. Applicants MUST apply for this position on-line at https://jobs.ou.edu. Search for the job requisition #16316 (Scientist/Researcher II). The position is available immediately and will remain open until filled. For further information, please contact Dr. Ann West by phone (405) 325-1529 or email aw...@ou.edu. The University of Oklahoma is an equal opportunity institution. www.ou.edu/eoo Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmtho...@ou.edu http://barlywine.chem.ou.edu http://structuralbiology.ou.edu
Re: [ccp4bb] SHELX-2013 release and homepage
The underlying issue is that the implementation of OS X dynamic linking is dependent system architecture. As I understand it, OS X 10.5.8 has a 32 bit kernel, so its dynamic linking is not forward-compatible with 64 bit OS X versions, for which SHELX-2013 seems to built. Also, to be fair, it's not as if Linux users have ever been able to migrate from from 32 bit to 64 bit without a complete system overhaul. So while I believe that OS X may not be the optimal OS of the future, the 32/64 bit incompatibility should not be blamed as the reason. James p.s. What I don't understand is why the dynamic loader was ever needed in the first place. As a zero dependency program, wouldn't it make sense just to statically compile all of the SHEL* programs at the cost of a little bigger downloads? On Feb 27, 2013, at 3:10 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 phew - and people claim, macs were user-friendly. On Linux you just add '-static' (at least for command line tools as the shelx programs) and make the sane assumption that the kernel is less than say 10 years old... Tim On 02/26/2013 04:50 PM, Guangyu Zhu wrote: I just downloaded it. I'm using Mac 10.5.8 and getting error messages: dyld: unknown required load command 0x8022 Trace/BPT trap Google search shows that: You should contact the developer of this application. Only the developer can fix this. The application was incorrectly built on a OS X 10.6 machine for a OS X 10.5 machine. The developer can fix this by considering three things: 1. Using the correct compiler parameters: gcc-4.2 -mmacosx-version-min=10.5 -isysroot /Developer/SDKs/MacOSX10.5.sdk ... 2. Using the correct linker settings (setting environment variable before link command). This is required, so that the OS X 10.6 linker will not use the loader command 'LC_DYLD_INFO_ONLY' (=0x8022), because OS X 10.5 does not understand this command: export MACOSX_DEPLOYMENT_TARGET=10.5 (or setenv MACOSX_DEPLOYMENT_TARGET=10.5) After this is fixed, one can check if the application was correctly built for OS X 10.5 by running 'otool': otool -l binary The correct binary should not contain any 'LC_DYLD_INFO_ONLY' load commands (only 'LC_DYLD_INFO' commands). (also see my blog article http://grauonline.de/wordpress/?p=71 ) Is it possible to build one for Mac 10.5.8? Thanks! Guangyu Zhu On 2/26/13 3:32 AM, George Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: As some of you have already discovered, there is a major new release of the whole of SHELX (the first since 1997) complete with a new homepage that should make downloads easier. To obtain the programs, please point your browser to: http://shelx.uni-ac.gwdg.de/SHELX/ and then 'register' (top of blue menu, upper left). You will then receive the password immediately by email and can then go to 'downloads'. The procedure has been designed to make life difficult for spammers etc. A little program (in FORTRAN of course) turns the registrations into a sorted users' list, which I hand-edit where necessary before it appears on the homepage, this may take a few days. The homepage also provides access to extensive documentation, FAQs etc. Please let me know of any problems (even typos) with the homepage and programs, with so much new material there are sure to be some bugs. The new versions replace all previous versions including beta-tests and almost all the programs have been improved since their last beta-test version (see 'recent changes'). In particular, the new shelxe_2013/2 corrects a couple of serious bugs in the autotracing from MR models and MRSAD present in the beta-test 2013/1. George -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 - -- - -- 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 Mozilla - http://enigmail.mozdev.org/ iD8DBQFRLduMUxlJ7aRr7hoRAkNUAJ99nANlYCXYmlOqTpvKnDJyg+A1bwCdF7GA Ag8n9o/IzBAkuX+HBfH8cMw= =WBV3 -END PGP SIGNATURE-
Re: [ccp4bb] SHELX-2013 release and homepage
After consulting several Mac users, I decided that there were very few 32-bit Mac operating systems still in use by crystallographers, so (as stated on the new SHELX homepage) I am only providing a 64-bit executables for Macs. The Mac executables do not run on old Macs with PPC processors either. For Linux and Windows I provide both 32 and 64-bit versions. One problem is that even if I tried to cross-compile a 32-bit version for Macs (with -m32 on the ifort compile/link command line?), I would have no way of testing it, and I would not wish to distribute untested programs. It might destroy SHELX's reputation for robustness. All SHELX programs in this release are as far as physically possible statically linked, which explains why the executables are large (though the Intel MKL FFT can take some of the blame for that too). Static linking is an essential part of the SHELX 'zero dependencies' philosophy. Apart from some trivial problems like some programs pretending to be beta-test versions when in fact they are the final release (I had simply forgotten to change the text), the complaint by Zhu was the only significant problem reported from the first ca. 500 downloads. There was however a problem in registering for the programs via the homepage using iPhones, but I think that I have managed to fix that now (I don't possess an iPhone or any other cell phone). However I would be very grateful to hear if anyone encounters difficulties with the new release or the homepage, there is so much new material in the homepage that there must be plenty of typos. George On 02/27/2013 11:21 PM, James Stroud wrote: The underlying issue is that the implementation of OS X dynamic linking is dependent system architecture. As I understand it, OS X 10.5.8 has a 32 bit kernel, so its dynamic linking is not forward-compatible with 64 bit OS X versions, for which SHELX-2013 seems to built. Also, to be fair, it's not as if Linux users have ever been able to migrate from from 32 bit to 64 bit without a complete system overhaul. So while I believe that OS X may not be the optimal OS of the future, the 32/64 bit incompatibility should not be blamed as the reason. James p.s. What I don't understand is why the dynamic loader was ever needed in the first place. As a zero dependency program, wouldn't it make sense just to statically compile all of the SHEL* programs at the cost of a little bigger downloads? On Feb 27, 2013, at 3:10 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 phew - and people claim, macs were user-friendly. On Linux you just add '-static' (at least for command line tools as the shelx programs) and make the sane assumption that the kernel is less than say 10 years old... Tim On 02/26/2013 04:50 PM, Guangyu Zhu wrote: I just downloaded it. I'm using Mac 10.5.8 and getting error messages: dyld: unknown required load command 0x8022 Trace/BPT trap Google search shows that: You should contact the developer of this application. Only the developer can fix this. The application was incorrectly built on a OS X 10.6 machine for a OS X 10.5 machine. The developer can fix this by considering three things: 1. Using the correct compiler parameters: gcc-4.2 -mmacosx-version-min=10.5 -isysroot /Developer/SDKs/MacOSX10.5.sdk ... 2. Using the correct linker settings (setting environment variable before link command). This is required, so that the OS X 10.6 linker will not use the loader command 'LC_DYLD_INFO_ONLY' (=0x8022), because OS X 10.5 does not understand this command: export MACOSX_DEPLOYMENT_TARGET=10.5 (or setenv MACOSX_DEPLOYMENT_TARGET=10.5) After this is fixed, one can check if the application was correctly built for OS X 10.5 by running 'otool': otool -l binary The correct binary should not contain any 'LC_DYLD_INFO_ONLY' load commands (only 'LC_DYLD_INFO' commands). (also see my blog article http://grauonline.de/wordpress/?p=71 ) Is it possible to build one for Mac 10.5.8? Thanks! Guangyu Zhu On 2/26/13 3:32 AM, George Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: As some of you have already discovered, there is a major new release of the whole of SHELX (the first since 1997) complete with a new homepage that should make downloads easier. To obtain the programs, please point your browser to: http://shelx.uni-ac.gwdg.de/SHELX/ and then 'register' (top of blue menu, upper left). You will then receive the password immediately by email and can then go to 'downloads'. The procedure has been designed to make life difficult for spammers etc. A little program (in FORTRAN of course) turns the registrations into a sorted users' list, which I hand-edit where necessary before it appears on the homepage, this may take a few days. The homepage also provides access to extensive documentation, FAQs etc. Please let me know of any problems (even typos) with the homepage and programs, with so much new material there are sure to be some
[ccp4bb] Rfree flag
Dear users, Is it mandatory to use the same reflections for Rfree calculations of a ligand bound data as that of its native? Thank you With Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Rfree flag
Dear Kavya, It is not so. It is not mandatory. best, Sekar Dear users, Is it mandatory to use the same reflections for Rfree calculations of a ligand bound data as that of its native? Thank you With Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Could you kindly confirm the safe receipt of this mail please All best wishes and regards, Yours sincerely, Dr. K. Sekar, Ph.D. Associate Professor Bioinformatics Indian Institute of Science Bangalore 560 012 INDIA E-mail: se...@physics.iisc.ernet.in Tel: 91-(0)80-22933059, 23601409, 22932469 Fax:91-(0)80-23600683, 23600551 Homepage: http://www.physics.iisc.ernet.in/~dichome/sekhome/index.html -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] disulfide engineering
Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina
Re: [ccp4bb] Rfree flag
Hello, I think this depends on the type of problem you are facing: if the 2 crystals are not isomorphous then you cannot have the same R-free sets; if the 2 crystals are isomorphous then either you do not worry about keeping the same R-free set (but then the starting structure must be perturbed enough to get rid of R-free bias during refinement), or you keep the same indices for the reflections in the 2 R-free sets (same reflections in your message) in which case there is no R-free bias at the beginning of refinement. By R-free bias I mean this: in your new (liganded) crystal form, there are reflections that have seen the Fo's during refinement of the native structure but that are in the R-free set in the ligand structure. This leads to bias. HTH, Fred. On 28/02/13 06:54, Kavyashree Manjunath wrote: Dear users, Is it mandatory to use the same reflections for Rfree calculations of a ligand bound data as that of its native? Thank you With Regards Kavya -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] Rfree flag
Although it is not mandatory, I think it would be a very good idea, especially if you have the exact same spacegroup and the native and ligand-bound forms of your protein are essentially the same. If you do not use the same reflections, you are actually not reporting an independent (free) R-factor. Best regards, Folmer 2013/2/28 Prof. K. Sekar se...@physics.iisc.ernet.in Dear Kavya, It is not so. It is not mandatory. best, Sekar Dear users, Is it mandatory to use the same reflections for Rfree calculations of a ligand bound data as that of its native? Thank you With Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Could you kindly confirm the safe receipt of this mail please All best wishes and regards, Yours sincerely, Dr. K. Sekar, Ph.D. Associate Professor Bioinformatics Indian Institute of Science Bangalore 560 012 INDIA E-mail: se...@physics.iisc.ernet.in Tel: 91-(0)80-22933059, 23601409, 22932469 Fax:91-(0)80-23600683, 23600551 Homepage: http://www.physics.iisc.ernet.in/~dichome/sekhome/index.html -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Folmer Fredslund
