[ccp4bb] Tenure track position at Vanderbilt Univ.
Dear colleagues, I wanted to highlight a tenure track job that may appeal to structural biologists, biochemists, and/or biophysicists. Happy to answer any questions you may have. Best, Lauren Vanderbilt University invites applications for a tenure-track, faculty position in evolutionary biochemistry at the Assistant Professor rank. Investigators that apply experimental, engineering, and/or computational approaches to understand a) how proteins or other structural and catalytic features of cells evolve or b) how metabolic pathways evolve are particularly encouraged to apply. The selected candidate will join the Department of Biological Sciences (https://as.vanderbilt.edu/biosci/) and the Vanderbilt Evolutionary Studies Initiative (https://www.vanderbilt.edu/evolution/), with opportunities for a dual appointment in the Department of Chemistry (https://www.vanderbilt.edu/chemistry/) and affiliation with the Department of Biochemistry (https://medschool.vanderbilt.edu/biochemistry/) and the Center for Structural Biology (https://www.vanderbilt.edu/csb/). The candidate will be expected to develop an independent laboratory research program that complements current departmental and institutional strengths in evolution, biochemistry, genome science, biophysics, cell and molecular biology, chemical biology, synthetic chemistry, drug discovery, computational biology, host-microbe interactions, and neurobiology. As a new faculty member, the candidate will play an integral role within the trans-institutional Vanderbilt Evolutionary Studies Initiative and will benefit from collaborations with diverse internationally recognized programs, centers, and institutes. Top candidates will demonstrate excellence in research, highly effective teaching and mentoring to undergraduate and graduate students, and a desire to contribute to a collaborative academic community. Applicants must have earned a Ph.D. no later than August 16, 2022, and preferably one or more years of postdoctoral research experience. Applicants should submit: (a) a letter of interest, (b) full curriculum vitae, (c) a statement of research interests, (d) a statement of teaching philosophy, and (e) a statement of equity, diversity, and inclusion directly to http://apply.interfolio.com/93130. Applicants should arrange for at least three letters of recommendation to be sent to the same link. Completed applications must be received no later than October 15, 2021. Vanderbilt University is an Equal Opportunity/ Affirmative Action employer, embraces diversity and inclusion, and has a strong institutional commitment to recruiting and retaining an academically and culturally diverse community of faculty and to teaching students who are diversified by gender, race/ethnicity, and other social locations. Minorities, women, individuals with disabilities, and members of other underrepresented groups are strongly encouraged to apply. Vanderbilt University ranks in the top 15 National Universities and is located in the heart of Music City, Nashville, TN. Nashville is consistently rated as a great place to live (https://www.vanderbilt.edu/nashville/). Lauren Parker Jackson, Ph.D. Assistant Professor of Biological Sciences & Biochemistry Vanderbilt University Nashville, TN, USA http://www.jackson-lab.com/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
Hi Robbie I also use them quite regularly (less so coordconv, although I do use it), typically from the command line Thanks, Alejandro > On Aug 30, 2021, at 17:38, James Holton wrote: > > I use pdbset, coordconv and sftools a LOT. Usually for things no other > programs do, like converting to fractional coordinates, and performing math > operations on mtz data. Always from command line scripts. > > -James Holton > MAD Scientist > > On 8/26/2021 3:29 AM, Robbie Joosten wrote: >> Dear CCP4 users, >> >> We (as in, the CCP4 developers) are investigating some (potentially) missing >> functionality in CCP4i2 and/or Cloud with respect to the programs pdbset, >> pdbcur, coordconv, and sftools. Some of these tools are quite old and may >> need to be replaced by other tools with similar functionality. Could you >> answer a few questions: >> >> - Do you use any of these tools? >> - If so, how often? (Few times a week, month, year, or less than once a >> year). >> - Which functionality of program X do you use? >> - Would you like a graphical interface to that functionality or are you >> happy to use the command line? >> >> Personal example: >> I use pdbset a few times a month, but only the "noise" function. I don't >> need a graphical interface for it (because it is used in the context of >> pdb-redo). I also use sftools, "reduce -> merge average" a few times a year. >> Again, only from the command line. >> >> >> Feel free to send your answers directly to me or to the bulletin board if >> you want to start a discussion. Tips on alternative CCP4 tools to achieve >> similar effects are probably also interesting for other BB users. >> >> Cheers, >> Robbie >> >> >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >> list hosted by www.jiscmail.ac.uk, terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
I use pdbset, coordconv and sftools a LOT. Usually for things no other programs do, like converting to fractional coordinates, and performing math operations on mtz data. Always from command line scripts. -James Holton MAD Scientist On 8/26/2021 3:29 AM, Robbie Joosten wrote: Dear CCP4 users, We (as in, the CCP4 developers) are investigating some (potentially) missing functionality in CCP4i2 and/or Cloud with respect to the programs pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old and may need to be replaced by other tools with similar functionality. Could you answer a few questions: - Do you use any of these tools? - If so, how often? (Few times a week, month, year, or less than once a year). - Which functionality of program X do you use? - Would you like a graphical interface to that functionality or are you happy to use the command line? Personal example: I use pdbset a few times a month, but only the "noise" function. I don't need a graphical interface for it (because it is used in the context of pdb-redo). I also use sftools, "reduce -> merge average" a few times a year. Again, only from the command line. Feel free to send your answers directly to me or to the bulletin board if you want to start a discussion. Tips on alternative CCP4 tools to achieve similar effects are probably also interesting for other BB users. Cheers, Robbie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
Dear Eleanor, Thanks for pointing out that CCP4 FreeRflag selects the test set in the highest possible symmetry for the crystal class! I didn't know that. The following sentences (which are somewhat difficult to understand for me) in https://www.ccp4.ac.uk/html/freerflag.html appear to document that: "The FreeR_flag is randomly and uniformly distributed reflexion-by-reflexion, but, additionally, if the keyword NOSYM is not set, all reflections that are equivalent by the symmetry of the point group of the twin lattice (assuming the data is twinned), obtain the same flag. This includes both the possibility of merohedral and pseudomerohedral twinning. In the latter case, the obliquity parameter can be set using the keyword OBL." I wonder since which CCP4 version (or date) this is the default behaviour. best wishes, Kay On Mon, 30 Aug 2021 18:28:23 +0100, Eleanor Dodson wrote: >Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs >in the highest possible symmetry for the crystal class - eh P6/mmm for a >trigonal crystal, and expand the set to fill the actual space group. This >means the Free R assignment is suitable if later the crystal symmetry is >reassigned. But this was not always done in the past so if you are trying >to reuse free/work assignments from an old project there are possibilities >of not getting this. Maybe the best solution is to just generate a new Free >R set ? >Eleanor > ... To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
Dear Robbie, I don't use ccp4 regularly (since our structures are mainly small molecule structures), but when I do, I often use pdbset. I use it to remove het-atoms, or side chains, or water molecules, or reset the B-value. I also use sftools. I have a script for calculating Rcomplete with refmac. This script makes use of sftools in the preparation of the mtz-file. I use these tools, because they are command line tools - much faster than GUI based versions. Best wishes, Tim On Thu, 26 Aug 2021 10:29:22 + Robbie Joosten wrote: > Dear CCP4 users, > > We (as in, the CCP4 developers) are investigating some (potentially) > missing functionality in CCP4i2 and/or Cloud with respect to the > programs pdbset, pdbcur, coordconv, and sftools. Some of these tools > are quite old and may need to be replaced by other tools with similar > functionality. Could you answer a few questions: > > - Do you use any of these tools? > - If so, how often? (Few times a week, month, year, or less than once > a year). > - Which functionality of program X do you use? > - Would you like a graphical interface to that functionality or are > you happy to use the command line? > > Personal example: > I use pdbset a few times a month, but only the "noise" function. I > don't need a graphical interface for it (because it is used in the > context of pdb-redo). I also use sftools, "reduce -> merge average" a > few times a year. Again, only from the command line. > > > Feel free to send your answers directly to me or to the bulletin > board if you want to start a discussion. Tips on alternative CCP4 > tools to achieve similar effects are probably also interesting for > other BB users. > > Cheers, > Robbie > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ pgpenZJvWEENL.pgp Description: OpenPGP digital signature
Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
Dear Andrew, what I meant is "Everything else being equal, bad data result in a larger Rfree-Rwork gap than good data". Of course the gap also depends on the resolution, and other factors. best wishes, Kay On Mon, 30 Aug 2021 16:59:12 +0100, Andrew Leslie - MRC LMB wrote: >Dear Kay and Jon, > >I cannot remember Ian Tickles original posting on this (assuming that it was >made to the bulletin board), but surely the resolution of the data is also a >very important factor in the danger of over-fitting. The lower the resolution, >the worse the experimental data to refined parameter ratio becomes, and the >more likely it is to obtain an overfitted model, regardless of how accurate >that data might be. Perhaps this is why Kay said “generally I agree that the >accuracy of the data is inversely related to the danger of overfitting”, or >did you have something else in mind Kay? > >Cheers, > >Andrew > >> On 30 Aug 2021, at 13:59, Kay Diederichs >> wrote: >> >> Hi Jon, >> >> generally I agree that the accuracy of the data is inversely related to the >> danger of overfitting, and that selection in shells is not necessary. >> But if twinning is suspected, as here, and/or a choice between high and low >> symmetry spacegroup has to be made, one has to make sure that >> potentially symmetry-related reflections are _either_ labelled as test _or_ >> as work; a mixture will artificially down-bias Rfree. >> >> Selecting the test set in the highest possible symmetry (which is what >> Phenix does) is a good solution. This test set should be symmetry-expanded >> when trying the low-symmetry spacegroup (if one wants to compare R values). >> The latter is not necessary when working with thin shells - but that has >> other disadvantages. >> >> best wishes, >> Kay >> >> On Sun, 29 Aug 2021 14:32:34 +, Jon Cooper >> wrote: >> >>> Hello Engin, we discussed this a year or two ago in relation to NCS when >>> Ian Tickle convinced me that since overfitting is due errors in the data, >>> there is no reason to expect these errors to be correlated by NCS and >>> picking the R-free set uniformally or in shells doesn't matter. No doubt my >>> incompetence, but I can't see why twinning would be different. >>> >>> Cheers, Jon.C. >>> >>> Sent from ProtonMail mobile >>> >>> Original Message >>> On 29 Aug 2021, 05:32, Engin Özkan wrote: >>> Hi, I believe this is taken care of automatically if you use phenix to pick your free reflections. From http://www.phenix-online.org/documentation/tutorials/twinning.html "When a test set is designed, care must be taken that free and work reflections are not related by a twin law. The R-free set assignment in phenix.refine and phenix.reflection_file_converter is designed with this in mind: the free reflections are chosen to obey the highest possible symmetry of the lattice." I believe this applies to all datasets, just in case there may be twinning. Engin >> ... >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >> list hosted by www.jiscmail.ac.uk, terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ > > > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >list hosted by www.jiscmail.ac.uk, terms & conditions are available at >https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs in the highest possible symmetry for the crystal class - eh P6/mmm for a trigonal crystal, and expand the set to fill the actual space group. This means the Free R assignment is suitable if later the crystal symmetry is reassigned. But this was not always done in the past so if you are trying to reuse free/work assignments from an old project there are possibilities of not getting this. Maybe the best solution is to just generate a new Free R set ? Eleanor On Mon, 30 Aug 2021 at 16:59, Andrew Leslie - MRC LMB < and...@mrc-lmb.cam.ac.uk> wrote: > Dear Kay and Jon, > > I cannot remember Ian Tickles original posting on this (assuming that it > was made to the bulletin board), but surely the resolution of the data is > also a very important factor in the danger of over-fitting. The lower the > resolution, the worse the experimental data to refined parameter ratio > becomes, and the more likely it is to obtain an overfitted model, > regardless of how accurate that data might be. Perhaps this is why Kay said > “generally I agree that the accuracy of the data is inversely related to > the danger of overfitting”, or did you have something else in mind Kay? > > Cheers, > > Andrew > > > On 30 Aug 2021, at 13:59, Kay Diederichs > wrote: > > > > Hi Jon, > > > > generally I agree that the accuracy of the data is inversely related to > the danger of overfitting, and that selection in shells is not necessary. > > But if twinning is suspected, as here, and/or a choice between high and > low symmetry spacegroup has to be made, one has to make sure that > > potentially symmetry-related reflections are _either_ labelled as test > _or_ as work; a mixture will artificially down-bias Rfree. > > > > Selecting the test set in the highest possible symmetry (which is what > Phenix does) is a good solution. This test set should be symmetry-expanded > when trying the low-symmetry spacegroup (if one wants to compare R values). > > The latter is not necessary when working with thin shells - but that has > other disadvantages. > > > > best wishes, > > Kay > > > > On Sun, 29 Aug 2021 14:32:34 +, Jon Cooper < > jon.b.coo...@protonmail.com> wrote: > > > >> Hello Engin, we discussed this a year or two ago in relation to NCS > when Ian Tickle convinced me that since overfitting is due errors in the > data, there is no reason to expect these errors to be correlated by NCS and > picking the R-free set uniformally or in shells doesn't matter. No doubt my > incompetence, but I can't see why twinning would be different. > >> > >> Cheers, Jon.C. > >> > >> Sent from ProtonMail mobile > >> > >> Original Message > >> On 29 Aug 2021, 05:32, Engin Özkan wrote: > >> > >>> Hi, > >>> > >>> I believe this is taken care of automatically if you use phenix to pick > >>> your free reflections. > >>> > >>> From > http://www.phenix-online.org/documentation/tutorials/twinning.html > >>> > >>> "When a test set is designed, care must be taken that free and work > >>> reflections are not related by a twin law. The R-free set assignment in > >>> phenix.refine and phenix.reflection_file_converter is designed with > this > >>> in mind: the free reflections are chosen to obey the highest possible > >>> symmetry of the lattice." > >>> > >>> I believe this applies to all datasets, just in case there may be > twinning. > >>> > >>> Engin > >>> > > ... > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
Dear Kay and Jon, I cannot remember Ian Tickles original posting on this (assuming that it was made to the bulletin board), but surely the resolution of the data is also a very important factor in the danger of over-fitting. The lower the resolution, the worse the experimental data to refined parameter ratio becomes, and the more likely it is to obtain an overfitted model, regardless of how accurate that data might be. Perhaps this is why Kay said “generally I agree that the accuracy of the data is inversely related to the danger of overfitting”, or did you have something else in mind Kay? Cheers, Andrew > On 30 Aug 2021, at 13:59, Kay Diederichs > wrote: > > Hi Jon, > > generally I agree that the accuracy of the data is inversely related to the > danger of overfitting, and that selection in shells is not necessary. > But if twinning is suspected, as here, and/or a choice between high and low > symmetry spacegroup has to be made, one has to make sure that > potentially symmetry-related reflections are _either_ labelled as test _or_ > as work; a mixture will artificially down-bias Rfree. > > Selecting the test set in the highest possible symmetry (which is what Phenix > does) is a good solution. This test set should be symmetry-expanded when > trying the low-symmetry spacegroup (if one wants to compare R values). > The latter is not necessary when working with thin shells - but that has > other disadvantages. > > best wishes, > Kay > > On Sun, 29 Aug 2021 14:32:34 +, Jon Cooper > wrote: > >> Hello Engin, we discussed this a year or two ago in relation to NCS when Ian >> Tickle convinced me that since overfitting is due errors in the data, there >> is no reason to expect these errors to be correlated by NCS and picking the >> R-free set uniformally or in shells doesn't matter. No doubt my >> incompetence, but I can't see why twinning would be different. >> >> Cheers, Jon.C. >> >> Sent from ProtonMail mobile >> >> Original Message >> On 29 Aug 2021, 05:32, Engin Özkan wrote: >> >>> Hi, >>> >>> I believe this is taken care of automatically if you use phenix to pick >>> your free reflections. >>> >>> From http://www.phenix-online.org/documentation/tutorials/twinning.html >>> >>> "When a test set is designed, care must be taken that free and work >>> reflections are not related by a twin law. The R-free set assignment in >>> phenix.refine and phenix.reflection_file_converter is designed with this >>> in mind: the free reflections are chosen to obey the highest possible >>> symmetry of the lattice." >>> >>> I believe this applies to all datasets, just in case there may be twinning. >>> >>> Engin >>> > ... > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
Hi Jon, generally I agree that the accuracy of the data is inversely related to the danger of overfitting, and that selection in shells is not necessary. But if twinning is suspected, as here, and/or a choice between high and low symmetry spacegroup has to be made, one has to make sure that potentially symmetry-related reflections are _either_ labelled as test _or_ as work; a mixture will artificially down-bias Rfree. Selecting the test set in the highest possible symmetry (which is what Phenix does) is a good solution. This test set should be symmetry-expanded when trying the low-symmetry spacegroup (if one wants to compare R values). The latter is not necessary when working with thin shells - but that has other disadvantages. best wishes, Kay On Sun, 29 Aug 2021 14:32:34 +, Jon Cooper wrote: >Hello Engin, we discussed this a year or two ago in relation to NCS when Ian >Tickle convinced me that since overfitting is due errors in the data, there is >no reason to expect these errors to be correlated by NCS and picking the >R-free set uniformally or in shells doesn't matter. No doubt my incompetence, >but I can't see why twinning would be different. > >Cheers, Jon.C. > >Sent from ProtonMail mobile > > Original Message >On 29 Aug 2021, 05:32, Engin Özkan wrote: > >> Hi, >> >> I believe this is taken care of automatically if you use phenix to pick >> your free reflections. >> >> From http://www.phenix-online.org/documentation/tutorials/twinning.html >> >> "When a test set is designed, care must be taken that free and work >> reflections are not related by a twin law. The R-free set assignment in >> phenix.refine and phenix.reflection_file_converter is designed with this >> in mind: the free reflections are chosen to obey the highest possible >> symmetry of the lattice." >> >> I believe this applies to all datasets, just in case there may be twinning. >> >> Engin >> ... To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Joint iNEXT-Discovery and Instruct-ERIC call for access: protein production and protein characterisation or quantification of interactions
Dear all, The deadline for the the call for access to experimental facilities, integrating protein production services from Instruct-ERIC facilities and protein characterisation or quantification of interactions by the biophysics facilities of iNEXT-Discovery, is approaching. 10th of September 2021. As a quick reminder, our experts can help you produce the proteins (and complexes) that you are interested in and characterise the quality of these samples, by general assays (eg stability) or specific assays (eg ligand or DNA binding). If these look interesting, you can also access other services of Instruct-ERIC and iNEXT-Discovery to study further the structure and dynamics of these macromolecules (but these experiments should be included as parr of the initial plan, but can come later). Access costs will be covered by Instruct-ERIC and iNEXT-Discovery, subject to successful external peer review. Exceptionally, we are considering and supporting also applications from non-Instruct member countries. Please apply at: https://joint.inext-discovery.eu/submit-proposal/ We look forward receiving your applications - with best regards from the Instruct-ERIC and iNEXT-Discovery teams, Tassos To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
