[ccp4bb] The 10% Gap between R-factor and R-free
Good Morning to ALL, I encountered large gaps between R-factor and R-free, eg. 10% and 11%, during refining several structures with either Refmac or Phenix.refine. The data were reduced and scaled at resolution with I/SIGMA higher than 2.3. The model fits and density pretty well despite a few side chains missing density. I may ask for the reasons that result in such large difference between R and R free and some ways to examine and improve the refinement. Thanks in advance Wenhua Univ. Paris-Sud XI, Orsay On 11/25/2013 6:03 PM, Beatrice Vallone wrote: Please check the announcement for 2014 ESRF Users' Meeting Associated Structural Biology Workshop. Invitation to the 2014 ESRF Users' Meeting Associated Workshops to meet and discuss with fellow users, get inspired, establish new scientific collaborations and learn about future opportunities offered by the ESRF for your research. Workshop on*Structural Biology at ESRF: Past, Present Future http://www.esrf.eu/home/events/conferences/um2014/structural-biology-workshops.html* 3 - 5 February The Plenary Meeting will feature: *5 plenary lectures by world leading scientists covering a large spectrum of ESRF activities; * a presentation on the status of the facility and on the progress of the Upgrade Programme; * a talk by the winner of the prestigious ESRF Young Scientist Award; * a poster session; * a banquet, with awards to the ESRF Young Scientist Award and for the best poster Programs for the Meeting and Workshops are available at: http://www.esrf.eu/home/events/conferences/um2014.html Regards to all, Beatrice Vallone ESRF User Organization Committee
Re: [ccp4bb] The 10% Gap between R-factor and R-free
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wenhua, a large gap between R1 and Rfree is often inficative for overfitting. Take a look at the following: - - how many water molecules are there in total? Do they all chamically make sense, do some of them have large B-values? Water molecules are the trash bin of any crystallographic model: it is easy to drop the R1-value by adding water molecules. - - do you have a good geometry (run molprobity)? Otherwise you should tighten the weight adding more weight to the geometry restraints. Having said this I noticed that refmac5 has greatly improved over the passed two years with respect to automated weighting. - - Do your B-values vary reasonably? There is a utility in coot displaying the B-factor variance along your structure. Again, if you are using refmac5, there should not be much of a problem here. - - Check the occupancies of your atoms. Recently I noticed a substantial number of PDB entries with occupancies varying within a molecule, sometimes even within one residue. This make no sense to me at all and again, even if there were a plausible explanation (e.g. hydrogen exchange in water molecules for neutron structures), the limited resolution of most structures in the PDB does not justify this variation. Best, Tim On 11/26/2013 09:49 AM, Wenhua Zhang wrote: Good Morning to ALL, I encountered large gaps between R-factor and R-free, eg. 10% and 11%, during refining several structures with either Refmac or Phenix.refine. The data were reduced and scaled at resolution with I/SIGMA higher than 2.3. The model fits and density pretty well despite a few side chains missing density. I may ask for the reasons that result in such large difference between R and R free and some ways to examine and improve the refinement. Thanks in advance Wenhua Univ. Paris-Sud XI, Orsay On 11/25/2013 6:03 PM, Beatrice Vallone wrote: Please check the announcement for 2014 ESRF Users' Meeting Associated Structural Biology Workshop. Invitation to the 2014 ESRF Users' Meeting Associated Workshops to meet and discuss with fellow users, get inspired, establish new scientific collaborations and learn about future opportunities offered by the ESRF for your research. Workshop on*Structural Biology at ESRF: Past, Present Future http://www.esrf.eu/home/events/conferences/um2014/structural-biology-workshops.html* 3 - 5 February The Plenary Meeting will feature: *5 plenary lectures by world leading scientists covering a large spectrum of ESRF activities; * a presentation on the status of the facility and on the progress of the Upgrade Programme; * a talk by the winner of the prestigious ESRF Young Scientist Award; * a poster session; * a banquet, with awards to the ESRF Young Scientist Award and for the best poster Programs for the Meeting and Workshops are available at: http://www.esrf.eu/home/events/conferences/um2014.html Regards to all, Beatrice Vallone ESRF User Organization Committee - -- - -- 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/ iD8DBQFSlGZeUxlJ7aRr7hoRAhNwAJ9F3utsgf6uNMW80j5by1RHbyTAtQCfYkfV 2Xsl1cLsB4BPYuabWOqouHM= =NI2B -END PGP SIGNATURE-
Re: [ccp4bb] The 10% Gap between R-factor and R-free
Hi Wenhua You didn't say what resolution your structure is: that's critical to deciding how significant is the R-factor difference (or more strictly the ratio). There are other factors such as solvent content: generally anything which affects the obs/param ratio (such as NCS restraints) will also affect what value of Rfree you would expect to get given a value of Rwork, assuming purely random errors and a structure refined to convergence. Note that this doesn't tell you directly whether there's overfitting: that's more a matter of comparing results from different parameterisations weighting schemes. The value of Rwork itself will affect the Rfree-Rwork difference: higher values of Rwork tend to give higher Rfree-Rwork, other things being equal (using the Rfree/Rwork ratio instead of the difference normalises the difference and removes this dependence on Rwork). For example for 3A resolution or lower, a difference of 0.1 may not be indicative of a problem (depending as I said on the value of Rwork). At 1A it almost certainly would indicate a problem since at that resolution you would normally expect a ratio of say around 1.2 ( or a difference of around 0.02 for Rwork = 0.1). At 3A or lower resolution you expect a ratio of say 1.4 or more so you could easily get a difference of 0.1 for Rwork ~= 0.25. For anything in between these extremes we need a bit more info! Cheers -- Ian On 26 November 2013 08:49, Wenhua Zhang xtal.zh...@gmail.com wrote: Good Morning to ALL, I encountered large gaps between R-factor and R-free, eg. 10% and 11%, during refining several structures with either Refmac or Phenix.refine. The data were reduced and scaled at resolution with I/SIGMA higher than 2.3. The model fits and density pretty well despite a few side chains missing density. I may ask for the reasons that result in such large difference between R and R free and some ways to examine and improve the refinement. Thanks in advance Wenhua Univ. Paris-Sud XI, Orsay On 11/25/2013 6:03 PM, Beatrice Vallone wrote: Please check the announcement for 2014 ESRF Users' Meeting Associated Structural Biology Workshop. Invitation to the 2014 ESRF Users' Meeting Associated Workshops to meet and discuss with fellow users, get inspired, establish new scientific collaborations and learn about future opportunities offered by the ESRF for your research. Workshop on* Structural Biology at ESRF: Past, Present Future http://www.esrf.eu/home/events/conferences/um2014/structural-biology-workshops.html* 3 - 5 February The Plenary Meeting will feature: -5 plenary lectures by world leading scientists covering a large spectrum of ESRF activities; - a presentation on the status of the facility and on the progress of the Upgrade Programme; - a talk by the winner of the prestigious ESRF Young Scientist Award; - a poster session; - a banquet, with awards to the ESRF Young Scientist Award and for the best poster Programs for the Meeting and Workshops are available at: http://www.esrf.eu/home/events/conferences/um2014.html Regards to all, Beatrice Vallone ESRF User Organization Committee
Re: [ccp4bb] Refinement of data with pseudo translation symmetry
Well - your R values will probably appear higher than normal - there will be zones where all reflections are weak.. but the maximum likelihood targets are meant to deal with this reasonably well. It seems to work and the maps usually look OK! Eleanor On 25 November 2013 22:31, Niu Tou niutou2...@gmail.com wrote: Dear All, Does any body know if the existence of pseudo translation symmetry will affect refinement ? If it does, is there any keyword or method to avoid it? Thanks! Best, Niu
Re: [ccp4bb] Stereo monitor
Dear all, Thanks to all for the information, especially to Jeroen for the detailed comments and thanks to Kay for the Wiki link, that was really helpful! So one possible option among others seems to be: - NVIDIA Quadro K600 - Asus VG278HR Just to get it right: Although the K600 is listed under 'Windows only', here http://www.nvidia.com/object/3d-vision-pro-requirements.html#Quadro the card should work with 3D under Linux, since I will have the monitor with built-in emitter, correct? Many thanks and best wishes, Tobias. On Fri, Nov 22, 2013 at 10:03 AM, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: I'm using a 24 BenQ XL2420TX (emitter builit-in; price 500€) monitor connected to the DisplayPort of a Quadro FX 380 card. Works very well on 64bit ScientificLinux 6.4 with the kmod-nvidia driver from ElRepo. Please also see http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo . HTH, Kay -- ___ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Wolfgang-Pauli-Str. 10, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax:+41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias ___
[ccp4bb] Industrial Research from Young Scientists, 2014 ACA Meeting
The Industrial Special Interest Group and Young Scientists Special Interest Group of the American Crystallographic Association will be hosting a scientific session on Sunday, May 25, 2014 during the ACA Meeting in Albuquerque, New Mexico which will highlight research by young scientists (undergraduate, graduate, post-doc) that is done in industry or in collaboration with industry. We encourage young scientists in this area to submit an abstract for consideration for a talk during this session. A brief description of the session is highlighted below, 1.2.1 Industrial Research from Young ScientistsOrganizers: George Lountos, Pete Wood An industrial environment can provide invaluable research and career experience for students and other young scientists. At the same time a short or long term research placement can provide an industrial partner with the opportunity to have very focussed research carried out in an otherwise time-stretched setting. This session will showcase research being performed by young scientists at any level (undergraduate, post-graduate or early post-doctoral) either within industry or funded by industry. The deadline for abstract submission is January 31, 2014. Abstracts may be submitted online at http://www.amercrystalassn.org/2014-abstracts Young scientists wishing to present at the meeting are also encouraged to apply for a Travel Grant. http://www.amercrystalassn.org/2014-young-scientists If you have any questions, feel free to contact the session organizers, Pete Wood (w...@ccdc.cam.ac.uk) or George Lountos (lount...@mail.nih.gov) Thanks, George George Lountos, Ph.D.Basic Science ProgramLeidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederick, MD 21702
Re: [ccp4bb] The 10% Gap between R-factor and R-free
Hi Wenhua, concerning phenix.refine: just run it again with weights optimization and it should fix the problem (assuming everything else done right: such as you are using correct refinement strategy). If using weights optimization does not help then let me know off list or on Phenix mailing list and we will address this problem one way or another. Pavel On Tue, Nov 26, 2013 at 12:49 AM, Wenhua Zhang xtal.zh...@gmail.com wrote: Good Morning to ALL, I encountered large gaps between R-factor and R-free, eg. 10% and 11%, during refining several structures with either Refmac or Phenix.refine. The data were reduced and scaled at resolution with I/SIGMA higher than 2.3. The model fits and density pretty well despite a few side chains missing density. I may ask for the reasons that result in such large difference between R and R free and some ways to examine and improve the refinement. Thanks in advance Wenhua Univ. Paris-Sud XI, Orsay On 11/25/2013 6:03 PM, Beatrice Vallone wrote: Please check the announcement for 2014 ESRF Users' Meeting Associated Structural Biology Workshop. Invitation to the 2014 ESRF Users' Meeting Associated Workshops to meet and discuss with fellow users, get inspired, establish new scientific collaborations and learn about future opportunities offered by the ESRF for your research. Workshop on* Structural Biology at ESRF: Past, Present Future http://www.esrf.eu/home/events/conferences/um2014/structural-biology-workshops.html* 3 - 5 February The Plenary Meeting will feature: -5 plenary lectures by world leading scientists covering a large spectrum of ESRF activities; - a presentation on the status of the facility and on the progress of the Upgrade Programme; - a talk by the winner of the prestigious ESRF Young Scientist Award; - a poster session; - a banquet, with awards to the ESRF Young Scientist Award and for the best poster Programs for the Meeting and Workshops are available at: http://www.esrf.eu/home/events/conferences/um2014.html Regards to all, Beatrice Vallone ESRF User Organization Committee
Re: [ccp4bb] Stereo monitor
YES!, this new card will work (once properly set-up under linux). I triple checked the new k600 card actually has a dual-link DVI and it has. So, no problem linking it to the VG278HR. It is listed "windows only" because it lacks the 3-pin connector... but you will not need it because of the build in IR-emittter! - J. - Am 26.11.13 14:42, schrieb Tobias Beck: Dear all, Thanks to all for the information, especially to Jeroen for the detailed comments and thanks to Kay for the Wiki link, that was really helpful! So one possible option among others seems to be: - NVIDIA Quadro K600 - Asus VG278HR Just to get it right: Although the K600 is listed under 'Windows only', here http://www.nvidia.com/object/3d-vision-pro-requirements.html#Quadro the card should work with 3D under Linux, since I will have the monitor with built-in emitter, correct? Many thanks and best wishes, Tobias. On Fri, Nov 22, 2013 at 10:03 AM, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: I'm using a 24" BenQ XL2420TX (emitter builit-in; price 500€) monitor connected to the DisplayPort of a Quadro FX 380 card. Works very well on 64bit ScientificLinux 6.4 with the kmod-nvidia driver from ElRepo. Please also see http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo . HTH, Kay -- ___ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Wolfgang-Pauli-Str. 10, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax: +41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias ___ -- Dr. Jeroen R. Mesters Deputy and Group Leader Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de http://www.iobcr.org -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. --
Re: [ccp4bb] Stereo monitor
Thanks! On Tue, Nov 26, 2013 at 5:03 PM, mesters mest...@biochem.uni-luebeck.dewrote: YES!, this new card will work (once properly set-up under linux). I triple checked the new k600 card actually has a dual-link DVI and it has. So, no problem linking it to the VG278HR. It is listed windows only because it lacks the 3-pin connector... but you will not need it because of the build in IR-emittter! - J. - Am 26.11.13 14:42, schrieb Tobias Beck: Dear all, Thanks to all for the information, especially to Jeroen for the detailed comments and thanks to Kay for the Wiki link, that was really helpful! So one possible option among others seems to be: - NVIDIA Quadro K600 - Asus VG278HR Just to get it right: Although the K600 is listed under 'Windows only', here http://www.nvidia.com/object/3d-vision-pro-requirements.html#Quadro the card should work with 3D under Linux, since I will have the monitor with built-in emitter, correct? Many thanks and best wishes, Tobias. On Fri, Nov 22, 2013 at 10:03 AM, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: I'm using a 24 BenQ XL2420TX (emitter builit-in; price 500€) monitor connected to the DisplayPort of a Quadro FX 380 card. Works very well on 64bit ScientificLinux 6.4 with the kmod-nvidia driver from ElRepo. Please also see http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo . HTH, Kay -- ___ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Wolfgang-Pauli-Str. 10, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax:+41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias ___ -- Dr. Jeroen R. Mesters Deputy and Group Leader Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de Http://www.biochem.uni-luebeck.de http://www.iobcr.org Http://www.iobcr.org -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. -- -- ___ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Wolfgang-Pauli-Str. 10, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax:+41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias ___ ggcagbjf.png
[ccp4bb] SSRL ; Can not access
Hi folks, I can not access to SSRL from yesterday. smbnxs1.slac.stanford.edu. or smbnxs2.slac.stanford.edu I wonder something is wrong in the server. Please let me know what happened to the SSRL if you know that. Thanks to all. Daniel
Re: [ccp4bb] SSRL ; Can not access
I just checked, and am logging on fine. Oli On Tue, Nov 26, 2013 at 9:40 AM, Daniel philoje...@gmail.com wrote: Hi folks, I can not access to SSRL from yesterday. smbnxs1.slac.stanford.edu. or smbnxs2.slac.stanford.edu I wonder something is wrong in the server. Please let me know what happened to the SSRL if you know that. Thanks to all. Daniel -- Dr. Oliver B. Zeldin Brunger Group Stanford University
[ccp4bb] Postdoctoral position, Edmonton (Canada)
Applications are invited for a postdoctoral position to work on crystallography of membrane-embedded enzymes. Experience in crystallography is preferred. In addition, the successful candidate should be well versed in one or more of the following areas: molecular biology, protein purification, and membrane protein biochemistry. The candidate must be within five years of attaining a PhD degree. This is an opportunity to join a lab experienced in the expression and crystallization of membrane proteins (See *PNAS *(2007) 104(3):750-4, and *Science, *(2003)*. *301:616-620),( http://www2.biochem.ualberta.ca/LemieuxLab/ ). The University of Alberta, located in Edmonton, Alberta (Canada), is home to a large and interactive community of biomedical scientists, and facilities for structural biology are excellent. Our department provides interaction with numerous crystallographers. A newly commissioned Canadian Light Source (CLS) synchrotron facility is located a short drive away. In addition, the membrane protein research group provides a dedicated forum for membrane protein research at the University of Alberta ( http://www.mprg.med.ualberta.ca/index.php ). Edmonton, having a population of over 1 million, offers a cosmopolitan environment with world-class performing arts, sports, culinary and recreational opportunities. In addition, the city’s proximity to the Rocky Mountains including the towns of Jasper and Banff is an additional bonus. Salary is commensurate with training and experience at the CIHR standard rates. A medical and dental benefit package is included with salary. The University of Alberta hires on the basis of merit. We are committed to the principle of equity in employment. We welcome diversity and encourage applications from all qualified women and men, including persons with disabilities, members of visible minorities, and Aboriginal persons. The records arising from this competition will be managed in accordance with provisions of the Alberta Freedom of Information and Protection of Privacy Act (FOIPP). Please direct cv's , statement of interests and three references to Dr. M. Joanne Lemieux at the following email address: joanne.lemi...@ualberta.cajoanne.lemi...@ualberta.ca . -- Joanne ** M. Joanne Lemieux, Ph.D. Assistant Professor, Canada Research Chair in Membrane Protein Structure and Function; AIHS Scholar Department of Biochemistry, Faculty of Medicine Dentistry, University of Alberta Medical Sciences Bldg. Office 4-53 Lab4-51 University of Alberta Edmonton AB, T6G 2H7 office phone: 780-492-3586 lab phone:780-492-3465 fax: 780-492-0886 Lab web page: http://www2.biochem.ualberta.ca/LemieuxLab http://www.biochem.ualberta.ca/faculty_detail.php?id=39# The 57th Annual Meeting of the Canadian Society for Molecular Biosciences April 2014: Membrane Protein in Health and Disease ( http://csmb-scbm.ca/meetings/57th_Annual_Conference.aspxhttp://www.poweredbynewgen.com/link.php?M=143337N=3862L=1631F=H ) Satellite meeting April 2014: Overcoming barriers in membrane protein structure http://www2.biochem.ualberta.ca/Trends2014/http://www2.biochem.ualberta.ca/Trends2013/ Membrane protein disease research group: http://www.mprg.med.ualberta.ca/index.php NSERC Membrane Training Group: www.MembraneTraining.ualberta.ca CONFIDENTIALITY WARNING This communication is intended for the use of the recipient to which it is addressed, and may contain confidential, personal, and/or privileged information. Please contact me immediately if you are not the intended recipient of this communication, and do not copy, distribute, or take action relying on it. Any communication received in error, or subsequent reply, should be deleted or destroyed.
[ccp4bb] trying to trace main chain of loop region in two alternative ways
Hello everyone, The electron density of my structure displays two alternative traces for the main chain in a loop region. Is there a way I can refine the structure with both the alternative main chains in place with 50% occupancy each? Thanks, Shy -- Shyamosree Bhattacharya 4th year Graduate Student Department of Chemistry Forest Lab 1550 Linden Drive Room No. 6541 Madison WI 53706
Re: [ccp4bb] trying to trace main chain of loop region in two alternative ways
I am using Refmac5 to refine my protein structure. Shy
