[ccp4bb] alpha lactose in COOT
Does anyone know why the ligand alpha lactose in COOT has at least one sugar ring that is not fully symmetrical. The CCDC deposited alpha lactose molecule has both rings perfectly symmetrical chairs. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] Temperature and crystallization
Dear Acoot, In the website of the company Centeo, you can find the slides of a short presentation I had given three years ago on temperature and macromolecular crystalllisation. You may find some info there: http://www.centeo.com/_fileupload/Temperature%20Control%20in%20PXTL.pdf There is a lot more on the centeo.com site. Best, Emmanuel Saridakis - Original Message - From: Acoot Brett To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, November 19, 2012 7:08 AM Subject: [ccp4bb] Temperature and crystallization Dear All, Will you please give a comment on how the temperature influences on the possibility to get protein crystal, and how the temperatures used to get the protein crystals of the same protein influences the protein 3-D structures of the same protein got based on the crystals of the same protein got at different temperatures? Cheers, Acoot
Re: [ccp4bb] hkl2000 install
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rui Wang, the window size of the main HKL2000 window is indeed fixed. One relatively simple workaround is to use a virtual screen size, provided you use X11. Check your /etc/X11/xorg.conf and add an entry, say, 'Virtual 1400 1024' in the Display Section and restart X - this way, as you hit the lower border of your monitor with the mouse pointer, to scroll down and see the lower parts of the HKL2000 window. Best, Tim On 11/19/2012 02:48 AM, 王瑞 wrote: OK,thank you all of you. I have installed one copy of HKL2000 on our desktop computer. But for my notebook's low 1366*768 resolution, the HKL2000 can't work ! So what could I do to resolve it ? 2012/11/13 王瑞 wangrui...@gmail.com: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang - -- - -- 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/ iD8DBQFQqgwaUxlJ7aRr7hoRAg3iAKDjrjBi1cpR07bszLOaZDMpHpBjmwCeI8i7 CcqbmAGU8rVWn7qqFJHo67w= =6s1F -END PGP SIGNATURE-
Re: [ccp4bb] CONECT Records
Thank you for the information. They are only coordination bonds between the atoms, which I wouldn't personally class as a physical bond. I am also using WinCoot which does not have the option for Make Link under the Modelling tab in Extensions. Is this a function of the Linux version?
[ccp4bb] coot, shelx res files and R32 (H32)
Dear Developers of Coot, I believe that coot has never been able to display the crystallographic symmetry of a R32:H shelxl .res file. As a result, water picking does not work properly for such a file. Everything else seems to work fine. This is not a huge problem, but it would be nice to be able to see symmetry atoms without loading the corresponding shelxl .pdb (which accidentally lacks the space group information anyway, so it has to be edited prior to loading). Again, not a big problem but I believe it is an easy fix in the code, so hopefully this will be done at some point in the future. Thank you, Petr Petr Leiman EPFL BSP-415 CH-1015 Lausanne Switzerland
Re: [ccp4bb] coot, shelx res files and R32 (H32)
shelxl-2012 does include the space group in a way that Coot understands when it writes a .pdb file. This version is in the final beta-testing stage with a lot of new features (mainly for small molecules) and no known bugs, so I hope to release it soon. If anyone would like to try it now please send me an email. George On 11/19/2012 02:13 PM, Petr Leiman wrote: Dear Developers of Coot, I believe that coot has never been able to display the crystallographic symmetry of a R32:H shelxl .res file. As a result, water picking does not work properly for such a file. Everything else seems to work fine. This is not a huge problem, but it would be nice to be able to see symmetry atoms without loading the corresponding shelxl .pdb (which accidentally lacks the space group information anyway, so it has to be edited prior to loading). Again, not a big problem but I believe it is an easy fix in the code, so hopefully this will be done at some point in the future. Thank you, Petr Petr Leiman EPFL BSP-415 CH-1015 Lausanne Switzerland -- 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
Re: [ccp4bb] hkl2000 install
On 11/18/12 20:48, 王瑞 wrote: OK,thank you all of you. I have installed one copy of HKL2000 on our desktop computer. But for my notebook's low 1366*768 resolution, the HKL2000 can't work ! So what could I do to resolve it ? http://www.pcworld.com/article/261763/samsung_shows_off_series_9_laptop_with_retina_matching_display.html Samsung Shows Off Series 9 Laptop With Retina-Matching Display 2560 x 1440 pixels in a 13 inch laptop -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] coot, shelx res files and R32 (H32)
Dear George, Thank you very much for your continuing development of the shelx suite. A lot of users (yours truly included) are happy to continue using .res files in coot. It's just the stupid R32/H32 spacegroup that causes coot to misbehave a little. And I am simply very surprised of why this bug has survived so many revisions of coot. Thank you, Petr On Nov 19, 2012, at 2:33 PM, George Sheldrick wrote: shelxl-2012 does include the space group in a way that Coot understands when it writes a .pdb file. This version is in the final beta-testing stage with a lot of new features (mainly for small molecules) and no known bugs, so I hope to release it soon. If anyone would like to try it now please send me an email. George On 11/19/2012 02:13 PM, Petr Leiman wrote: Dear Developers of Coot, I believe that coot has never been able to display the crystallographic symmetry of a R32:H shelxl .res file. As a result, water picking does not work properly for such a file. Everything else seems to work fine. This is not a huge problem, but it would be nice to be able to see symmetry atoms without loading the corresponding shelxl .pdb (which accidentally lacks the space group information anyway, so it has to be edited prior to loading). Again, not a big problem but I believe it is an easy fix in the code, so hopefully this will be done at some point in the future. Thank you, Petr Petr Leiman EPFL BSP-415 CH-1015 Lausanne Switzerland -- 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
[ccp4bb] Macromolecular Crystallography Beamline Scientist Position at NSLS-II
Beamline Scientist Position for Macromolecular Crystallography Beamlines at NSLS-II The Photon Sciences Directorate at Brookhaven National Laboratory is seeking an experienced scientist to support the development of a Microfocusing Macromolecular Crystallography Beamline (FMX) and a Highly Automated Macromolecular Crystallography Beamline (AMX) at the National Synchrotron Light Source II (NSLS-II), which is a new 3rd-generation synchrotron facility being constructed on Long Island, New York, with extremely high brightness and exceptional beam stability over a wide spectral range. As a scientific staff member reporting to the Group Leader for the FMX/ AMX beamlines in the Photon Division, the selected candidate will be part of a group of scientific and engineering staff to design and build a pair of state-of-the-art macromolecular crystallography beamlines and its associated scientific programs at NSLS-II. Responsibilities include interacting with the scientific user community to define the mission and technical scope of the beamlines, and supporting all aspects of the beamline design, construction, commissioning, and operations. Qualifications Required: * Ph.D. in structural biology, physics, biophysics, or a related field * At least two (2) years of post-doctoral experience in macromolecular crystallography at a synchrotron beamline * Experience in synchrotron-based research is required in one of three scientific areas: (1) high throughput macromolecular crystallography, (2) design and development of crystallography instrumentation and methods, or (3) operation of a macromolecular crystallography user program at a synchrotron * Excellent written and oral communications skills * The ability to interact effectively in a team environment with a diverse group of scientists, engineers, technical staff, and users. Qualifications Preferred: * Experience with experimental investigations at the micro- or nano scale * Experience in process automation and remote control * Experience with crystallographic data analysis and structure solving * Experience in the design and analysis of optical components * Prior experience in project planning, execution, and reporting. The selected candidate will be placed at the appropriate scientific level dependent upon depth and breadth of relevant knowledge and skills he or she brings to the position, as well as the amount of relevant experience. For more information, go to http://www.bnl.gov/HR/careers/ and see Job ID# 16236 or contact Dieter Schneider at schnei...@bnl.govmailto:schnei...@bnl.gov Deadline for applications is November 27, 2012.
Re: [ccp4bb] coot, shelx res files and R32 (H32)
On 19/11/12 13:13, Petr Leiman wrote: Dear Developers of Coot, I believe that coot has never been able to display the crystallographic symmetry of a R32:H shelxl .res file. As a result, water picking does not work properly for such a file. Everything else seems to work fine. This is not a huge problem, but it would be nice to be able to see symmetry atoms without loading the corresponding shelxl .pdb (which accidentally lacks the space group information anyway, so it has to be edited prior to loading). Again, not a big problem but I believe it is an easy fix in the code, so hopefully this will be done at some point in the future. And I am simply very surprised of why this bug has survived so many revisions of coot. Yes, it it old code. I did not know about this issue (or forgot about it - that's not impossible). Yes, it seems not too hard to fix. Paul.
Re: [ccp4bb] CONECT Records
On 19/11/12 11:12, Jenny Harmer wrote: Thank you for the information. They are only coordination bonds between the atoms, which I wouldn't personally class as a physical bond. I am also using WinCoot which does not have the option for Make Link under the Modelling tab in Extensions. Is this a function of the Linux version? Are we talking 0.7? Paul.
[ccp4bb] Off-topic: heterologous co-expression in yeast
Hi, We have been thinking of implementing recombinant protein expression in S. cerevisiae in our lab, and I would like to ask if there is a choice of vector designed for co-expression of any two intracellular binding partners, similarly to the pETduet-1 vector for E. coli. If you feel this is not of broad interest, please reply directly to me. I thank you for your input, Andre LB Ambrosio Laboratório Nacional de Biociências - LNBio CNPEM, Brazil
Re: [ccp4bb] Off-topic: heterologous co-expression in yeast
Hi Andre, There is set of plasmids allowing coexpression in yeast they are described in the following article Constructionand characterization of bidirectional expression vectors in Saccharomyces cerevisiae Aimin Li1,2, Zengshan Liu1, Qianxue Li2, Lu Yu1, Dacheng Wang2 Xuming Deng 1,2 in FEMS Yeast Res 8 (2008) 6–9 !c Those plasmids are designed for coexpression and use two different promoters a constitutive one (GPD) and a strong inducible one (GAL). You have several selection markers and they are shuttle vectors for easy manipulation and amplification in E. coli. Hope this helps. Best of luck -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry Boyer Hall room 356 611 Charles E Young Drive East Los Angeles CA 90095 office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu
Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?
To add another datapoint, a couple of weeks ago, I saw a friend's MacBook Pro (probably 2007) had a battery case open up just like that. My 17-inch MacBook Pro (2008) case is also bent in a million different ways, and I have already had to change the bottom case once (for $130, and at no labor cost, since they were also changing the fried-up video card which was recalled), as the laptop would not even close. The top case is also coming apart, but replacing that is not an option apparently, since it practically comes with the display. I change my battery frequently enough that, I guess my battery does not go up in flames. I have always thought that the unibody design was Apple addressing these issues, but seeing what happened to those MacBook Airs just depresses me. Engin On 11/19/2012 10:37 AM, Charles Pemble wrote: Hey Bill, I have had this happen on two separate occasions with old macbook body style. The first (2008) resulted in Apple replacing the battery for free without any hassle. The second time (2010) was significantly worse (see attached pic) – Apple said, That's normal wear and tear. After much debate about this being normal, the guy at the Genius bar suggested my only option was to purchase a new one. Cheers, Charlie _ Charles W. Pemble IV, Ph.D. Facility Manager, Duke Medical School Crystallography Research Scientist, DHVI Duke University 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pem...@duke.edu mailto:charles.pem...@duke.edu On Sat, Nov 17, 2012 at 7:28 PM, William G. Scott wgsc...@ucsc.edu mailto:wgsc...@ucsc.edu wrote: Hi folks: I'm trying to get a sense for how frequently this sort of thing occurs: That was a macbook air that served me well for four years, but then self-destructed. (I took it to the Apple store. They generously offered to repair it for $800 or to sell me a new one, and suggested this was normal if you leave the power cord attached after the battery charges, even while giving a lecture or seminar.) It strikes me as a bit dangerous. --Bill Scott William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA --
Re: [ccp4bb] coot, shelx res files and R32 (H32)
Hi Petr, Thanks for noting this - yes it has existed for a while, sad to say. (I was using the standard space group name to convert between clipper symmetry and mmdb symmetry - that was a mistake - I should have been using the Extended Hermann–Mauguin symbols). Fixed in r4489. Paul. On 19/11/12 14:17, Petr Leiman wrote: Dear George, Thank you very much for your continuing development of the shelx suite. A lot of users (yours truly included) are happy to continue using .res files in coot. It's just the stupid R32/H32 spacegroup that causes coot to misbehave a little. And I am simply very surprised of why this bug has survived so many revisions of coot. Thank you, Petr On Nov 19, 2012, at 2:33 PM, George Sheldrick wrote: shelxl-2012 does include the space group in a way that Coot understands when it writes a .pdb file. This version is in the final beta-testing stage with a lot of new features (mainly for small molecules) and no known bugs, so I hope to release it soon. If anyone would like to try it now please send me an email. George On 11/19/2012 02:13 PM, Petr Leiman wrote: Dear Developers of Coot, I believe that coot has never been able to display the crystallographic symmetry of a R32:H shelxl .res file. As a result, water picking does not work properly for such a file. Everything else seems to work fine. This is not a huge problem, but it would be nice to be able to see symmetry atoms without loading the corresponding shelxl .pdb (which accidentally lacks the space group information anyway, so it has to be edited prior to loading). Again, not a big problem but I believe it is an easy fix in the code, so hopefully this will be done at some point in the future.
[ccp4bb] ctruncate/scapepacktomtz : terminate called after throwing an instance of clipper::Message_fatal
Hi All, I am running the latest ccp4 ( auto-updated using the new autoupdate tool built into ccp4i) I was running what should be a routine scalepack to mtz conversion and I got an error which I have never seen before with ctruncate. When I run the same job with old truncate it succeeds. Any ideas what may be causing this. I hope I snipped the correct part of the error message. Thanks Hari *** * Information from CCP4Interface script *** The program run with command: /home/hari/ccp4-6.3-download/ccp4-6.3.0/bin/ctruncate -hklin /tmp/hari/B8-C7-A_P21_4_1_mtz.tmp -hklout /tmp/hari/B8-C7-A_P21_4_3_mtz.tmp -colin /*/*/\[IMEAN,SIGIMEAN\] -colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout B8-C7-A_P21 -nres 150 has failed with error message CCP4MTZfile - internal error terminate called after throwing an instance of 'clipper::Message_fatal' *** #CCP4I TERMINATION STATUS 0 CCP4MTZfile - internal error terminate called after throwing an instance of 'clipper::Message_fatal' #CCP4I TERMINATION TIME 19 Nov 2012 16:50:26 #CCP4I MESSAGE Task failed
[ccp4bb] occupancy vs. Bfactors
Hello all, I'm currently working on a structure which if I stub a certain side chain phenix/coot shows me a large green blob which looks strikingly similar to the side chain, when I put it in and run another refinement the blob turns red. Basically I was just playing around and I changed the occupancy of the side chain and now there are no complaints. But I was thinking, should I haven changed the Bfactors instead? Should I have left well enough alone? If I lower the occupancy manually and do not include alternate confirmations have I introduced modelling bias? Could someone recommend some good articles I could read on exactly how to correctly fix this problem. Thanks, GM
Re: [ccp4bb] occupancy vs. Bfactors
Hi Grant, sounds like you did the right thing (as far as I can guess given the amount of information you provided). In a nutshell, both, B-factors and occupancies, model disorder. The difference is that occupancies model larger scale disorder (such as distinct conformations) than B-factors (smearing due to temperature vibrations, etc). Perhaps in you case the side chain has several conformations among which you can see only one, and therefore it's valid to model it with occupancy less than 1 (I presume you refined one occupancy per all atoms in that side chain). Pavel On Mon, Nov 19, 2012 at 3:36 PM, GRANT MILLS gdmi...@students.latrobe.edu.au wrote: Hello all, I'm currently working on a structure which if I stub a certain side chain phenix/coot shows me a large green blob which looks strikingly similar to the side chain, when I put it in and run another refinement the blob turns red. Basically I was just playing around and I changed the occupancy of the side chain and now there are no complaints. But I was thinking, should I haven changed the Bfactors instead? Should I have left well enough alone? If I lower the occupancy manually and do not include alternate confirmations have I introduced modelling bias? Could someone recommend some good articles I could read on exactly how to correctly fix this problem. Thanks, GM
Re: [ccp4bb] occupancy vs. Bfactors
Hi Grant, This is part of the recurring side chain discussion. There is no consensus in the community about what the optimal approach is. In your current approach you are adding a model parameter (occupancy) to improve the fit with the experimental data (remove negative difference density). You should ask yourself whether you really need to add that parameter. Are you not overfitting? Is there any clear evidence that the atoms are not always there? The alternative model you propose (full occupancy, high B) has fewer parameters and explains more of the strucure (you account for all atoms the protein has, prior knowledge). This model probably also better reflects the uncertainty of the coordinates of the side chains involved. If your B-factor restraints are not too tight, the difference densitty should also disappear (equal explanation of the experimental data). To me that would be a better model. HTH, Robbie Date: Mon, 19 Nov 2012 23:36:56 + From: gdmi...@students.latrobe.edu.au Subject: [ccp4bb] occupancy vs. Bfactors To: CCP4BB@JISCMAIL.AC.UK Hello all, I'm currently working on a structure which if I stub a certain side chain phenix/coot shows me a large green blob which looks strikingly similar to the side chain, when I put it in and run another refinement the blob turns red. Basically I was just playing around and I changed the occupancy of the side chain and now there are no complaints. But I was thinking, should I haven changed the Bfactors instead? Should I have left well enough alone? If I lower the occupancy manually and do not include alternate confirmations have I introduced modelling bias? Could someone recommend some good articles I could read on exactly how to correctly fix this problem. Thanks, GM
