[ccp4bb] Position opening - Colgate University
Please find attached a description of a position opening at Colgate University that may be of interest to a protein crystallographer interested in working with undergraduates in a research-rich, research supportive environment. Colgate is equipped with an Oxford Diffraction home source, Gryphon dropsetter, and a Scorpion screen maker, as well as other essential tools for a teacher-scholar interested in protein structure and function. In addition, Colgate is also only 90 minutes from CHESS. Cheers, ___ Roger S. Rowlett Gordon & Dorothy Kline Professor, Emeritus Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 email: rrowl...@colgate.edu To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 colgate-u-position.pdf Description: Adobe PDF document
Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?
Refmac fills in the reflections that are given in the input MTZ file without observed amplitudes/intensities. So if you only want to fill in low resolution reflections you have to shape your MTZ file accordingly. This is non default behaviour because typically all missing reflections up to the resolution cut-off are added by using the program unique or a similar approach. Cheers, Robbie On 3 Aug 2019 10:32, Kay Diederichs wrote: Dear Ivan, On Thu, 1 Aug 2019 22:10:36 -0400, Ivan Shabalin wrote: >Dear CCP4BB, > >There seems to be a general consensus for extending data to higher >resolution to include as much meaningful data as possible. "Meaningful" >can be defined in different ways. I heard/read opinions such as 0.5 >CC1/2, 0.3 CC1/2, 0.15 CC1/2, This is numerology - why not 0.3 or 0.12345? The EM community has agreed on the "gold standard" of 0.143 for FSC which has a similar definition as CC1/2 - this value is chosen because the quantity analogous to CC* is then 0.5 ! > and stepped (paired) refinement. The >latter seems to be one of the most rigorous options according to many >crystallographers. > >Including more data sounds like a good thing, but, it sometimes results >in low completeness in high resolution shells. As far as i understand, >this may result from: > >a) anisotropic diffraction (if a software cuts of resolution in >non-isotropic way) > >b) sub-optimal data collection (e.g. due to limitations of the >instrument, such as minimum detector distance allowed, absence of kappa, >limits on oscillation range) > >In the commonly referred paper, the completeness is 96% in the highest >shell (Karplus, P. A., & Diederichs, K. (2012). Linking crystallographic >model and data quality. Science (New York, N.Y.), 336(6084), 1030–1033.) >In other words, these tests were performed for an almost complete dataset. > >I used to think that more data is always better, but, as I learned >recently from Clemens Vonrhein, the resulting low completeness may cause >model bias in the maps. ... due to "fill-in" of missing reflections which is performed by Refmac and phenix.refine (https://www.phenix-online.org/documentation/faqs/refine.html#general); don't know about other programs. >Indeed, REFMAC by default tries to restore missing reflections, which >are approximated as DFc >(https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html). > > >We tried using the keyword "mapcalculate free include" and "mapcalculate >free exclude" for one of our structures (~1.3A, P1), and it did seem to >improve the maps a little - we saw more meaningful features. > >But, I still have several questions: > >1) Does using "mapcalculate free include" in REFMAC represent a sound >solution to this problem? Does this "no fill-in at all" solution >constitute a significant problem? I think it would be desirable to "fill in" only the reflections missing at low resolution (e.g. in your case to 3A); that would improve the maps but decrease the model bias. Not sure if any program supports this. > >2) Are there any other concerns about using data with low completeness >in highest shells? no. To the contrary, even if the visual effect of weak reflections on the map may be low, the errors in the model coordinates will be less if the weak amplitudes (or even better, intensities - once the refinement programs use these) are used as restraints in refinement. > >3) STARANISO website suggests a way of handling this problem >(http://staraniso.globalphasing.org/test_set_flags_about.html). But, >would not REFMAC "fill-in" all the reflections for map coefficients >calculation to isotropic completeness anyway? > >4) What is your personal approach to handling this issue? Is there >completeness value in the last shell that is too low to include it in >Table 1? To me, the rule "the completeness in high-resolution shell is too low if it is less than XX %" appears not to be based on any appropriate concept. If there is good information in that resolution shell, it should be used no matter what the completeness is. Practically, this means that one has to devote a lot of attention to doing the experiment right, by choosing an appropriate crystal-detector distance. As always, attempts to computationally rectify problems that result from a poor experiment have their own caveats. Thanks for bringing this up! Kay > >Many thanks, > >Ivan > >With best regards, >Ivan Shabalin, Ph.D. >Research Scientist, >Department of Molecular Physiology and Biological Physics, >University of Virginia, >1340 Jefferson Park Avenue, Pinn Hall,Room 4223, >Charlottesville, VA 22908 >https://www.linkedin.com/in/shabalinig/ >https://minorlab.org/person/ivan_s/ > > > > > > > > > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?
Dear Ivan, On Thu, 1 Aug 2019 22:10:36 -0400, Ivan Shabalin wrote: >Dear CCP4BB, > >There seems to be a general consensus for extending data to higher >resolution to include as much meaningful data as possible. "Meaningful" >can be defined in different ways. I heard/read opinions such as 0.5 >CC1/2, 0.3 CC1/2, 0.15 CC1/2, This is numerology - why not 0.3 or 0.12345? The EM community has agreed on the "gold standard" of 0.143 for FSC which has a similar definition as CC1/2 - this value is chosen because the quantity analogous to CC* is then 0.5 ! > and stepped (paired) refinement. The >latter seems to be one of the most rigorous options according to many >crystallographers. > >Including more data sounds like a good thing, but, it sometimes results >in low completeness in high resolution shells. As far as i understand, >this may result from: > >a) anisotropic diffraction (if a software cuts of resolution in >non-isotropic way) > >b) sub-optimal data collection (e.g. due to limitations of the >instrument, such as minimum detector distance allowed, absence of kappa, >limits on oscillation range) > >In the commonly referred paper, the completeness is 96% in the highest >shell (Karplus, P. A., & Diederichs, K. (2012). Linking crystallographic >model and data quality. Science (New York, N.Y.), 336(6084), 1030–1033.) >In other words, these tests were performed for an almost complete dataset. > >I used to think that more data is always better, but, as I learned >recently from Clemens Vonrhein, the resulting low completeness may cause >model bias in the maps. ... due to "fill-in" of missing reflections which is performed by Refmac and phenix.refine (https://www.phenix-online.org/documentation/faqs/refine.html#general); don't know about other programs. >Indeed, REFMAC by default tries to restore missing reflections, which >are approximated as DFc >(https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html). > > > >We tried using the keyword "mapcalculate free include" and "mapcalculate >free exclude" for one of our structures (~1.3A, P1), and it did seem to >improve the maps a little - we saw more meaningful features. > >But, I still have several questions: > >1) Does using "mapcalculate free include" in REFMAC represent a sound >solution to this problem? Does this "no fill-in at all" solution >constitute a significant problem? I think it would be desirable to "fill in" only the reflections missing at low resolution (e.g. in your case to 3A); that would improve the maps but decrease the model bias. Not sure if any program supports this. > >2) Are there any other concerns about using data with low completeness >in highest shells? no. To the contrary, even if the visual effect of weak reflections on the map may be low, the errors in the model coordinates will be less if the weak amplitudes (or even better, intensities - once the refinement programs use these) are used as restraints in refinement. > >3) STARANISO website suggests a way of handling this problem >(http://staraniso.globalphasing.org/test_set_flags_about.html). But, >would not REFMAC "fill-in" all the reflections for map coefficients >calculation to isotropic completeness anyway? > >4) What is your personal approach to handling this issue? Is there >completeness value in the last shell that is too low to include it in >Table 1? To me, the rule "the completeness in high-resolution shell is too low if it is less than XX %" appears not to be based on any appropriate concept. If there is good information in that resolution shell, it should be used no matter what the completeness is. Practically, this means that one has to devote a lot of attention to doing the experiment right, by choosing an appropriate crystal-detector distance. As always, attempts to computationally rectify problems that result from a poor experiment have their own caveats. Thanks for bringing this up! Kay > >Many thanks, > >Ivan > >With best regards, >Ivan Shabalin, Ph.D. >Research Scientist, >Department of Molecular Physiology and Biological Physics, >University of Virginia, >1340 Jefferson Park Avenue, Pinn Hall,Room 4223, >Charlottesville, VA 22908 >https://www.linkedin.com/in/shabalinig/ >https://minorlab.org/person/ivan_s/ > > > > > > > > > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
