Oh dear - I didn’t mean to start this discussion - just to have a private moan to Ian tickle, but there are some reasons for the regret. First of all - column names had a meaning . For example a refmac hklout has labels f sigf Phic from delfphwt etc and just occasionally one likes to see some detail like how fom falls off with resolution.
Then sometimes one has three data sets from “identical” crystals and it would be nice to inspect how identical they are. cAD allows you to gather them together with appropriate column names and I can find that useful. Then there is the question of anomalous differences. We do much less expensive phasing now where SAD or MAD datasets are important but I almost always check the anom diff map at the end of refinement to make sure I haven’t called SO4 a low bfacter water and that the MET residues really fo have a SD atom. Even when the anomsignal is insignificant these often show up. On Thu, 16 Mar 2023 at 09:00, Paul Bond < 000030b0cd59fccb-dmarc-requ...@jiscmail.ac.uk> wrote: > I believe there are many advantages to storing things *internally* as > data objects with metadata instead of as columns of an MTZ file. How many > students know what FP,SIGFP mean? And how many know that the FP,SIGFP > columns in Refmac's HKLIN are not the same as the FP,SIGFP columns in > HKLOUT? In an interface you can give these much more friendly names such as > "observed amplitudes" and "amplitudes scaled by Refmac". The problem is > that people should not need to access the *internal *i2 files to get to > this data. Currently, you can export mini MTZs (containing only one data > object) at the bottom of each report and you can export a full MTZ from > Refmac using the Export MTZ button at the top of the interface, but > probably this issue can be solved by doing the following: > > 1. Making sure that reflection data objects have sensible names > 2. Expanding the "Export MTZ" functionality to have a customisable > selection of any data objects (and allowing customisation of column labels > as there may be clashes) > > Kind regards, > Paul > > On Thu, 16 Mar 2023 at 07:14, Jan Dohnalek <dohnalek...@gmail.com> wrote: > >> We are hitting the same problems also with students (so no rigidified >> brains I think) ... the concept of "files" seems absolutely natural (also >> to them) and when they ask about solving more tricky problems in i2 ... we >> do the obvious, go back to ccp4i. >> >> I2 is fine when things are smooth and easy. >> >> Jan >> >> >> On Wed, Mar 15, 2023 at 3:52 PM Randy John Read <rj...@cam.ac.uk> wrote: >> >>> Hi Jon, >>> >>> My understanding of the philosophy is that new users would prefer to >>> think about crystallographic data objects, rather than worrying about the >>> arcana of MTZ files and the many different flavours of columns. There are >>> tradeoffs — it can indeed be more difficult to find the bits of information >>> you need, but you should be thinking in terms of the stored objects from >>> the imports at the beginning of the project, rather than the files that >>> hold them. >>> >>> Personally, I find multicolumn MTZ files easier to think about, but my >>> brain probably rigidified a decade or two ago! >>> >>> Best wishes, >>> >>> Randy >>> >>> > On 15 Mar 2023, at 13:09, Jon Cooper < >>> 0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: >>> > >>> > Hello Ian, >>> > >>> > if I understand you and Eleanor correctly, this is the philosophy of >>> the mini-MTZ, i.e. if you are doing anything independent of i2, you have to >>> dig around a bit to find which output file contains the columns you need. >>> > >>> > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com >>> > >>> > Sent from Proton Mail mobile >>> > >>> > >>> > >>> > -------- Original Message -------- >>> > On 13 Mar 2023, 23:27, Ian Tickle < ianj...@gmail.com> wrote: >>> > >>> > >>> > Eleanor, which program is doing that and more to the point, why? >>> > >>> > -- Ian >>> > >>> > >>> > On Mon, 13 Mar 2023 at 20:17, Eleanor Dodson < >>> eleanor.dod...@york.ac.uk> wrote: >>> > fIf you are using ccp4I2 for some forgotten reason the final output >>> has one reflection with I+ and I-, another with Imean, another with Fmean - >>> aagghh >>> > >>> > >>> > On Mon, 13 Mar 2023 at 19:40, Ian Tickle <ianj...@gmail.com> wrote: >>> > >>> > Hi Gottfried >>> > >>> > AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default. >>> > >>> > Cheers >>> > >>> > -- Ian >>> > >>> > >>> > On Mon, 13 Mar 2023 at 18:53, Palm, Gottfried <p...@uni-greifswald.de> >>> wrote: >>> > Dear all, >>> > I have a few questions handling (non) anomalous data: >>> > By default aimless seems to produce Iplus and Iminus columns. Can I >>> force it to (also) create an Imean column? >>> > What does refmac do, when it gets Iplus and Iminus (and their sigmas) >>> as input. Does it take only one of them or does it calculate and use Imean? >>> > Greetings >>> > Gottfried >>> > >>> > To unsubscribe from the CCP4BB list, click the following link: >>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> > >>> > >>> > To unsubscribe from the CCP4BB list, click the following link: >>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> > >>> > >>> > To unsubscribe from the CCP4BB list, click the following link: >>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> > >>> > >>> > To unsubscribe from the CCP4BB list, click the following link: >>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> > >>> >>> ----- >>> Randy J. Read >>> Department of Haematology, University of Cambridge >>> Cambridge Institute for Medical Research Tel: +44 1223 336500 >>> The Keith Peters Building >>> Hills Road E-mail: >>> rj...@cam.ac.uk >>> Cambridge CB2 0XY, U.K. >>> www-structmed.cimr.cam.ac.uk >>> >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ >>> >> >> >> -- >> Jan Dohnalek, Ph.D >> Institute of Biotechnology >> Academy of Sciences of the Czech Republic >> Biocev >> Prumyslova 595 >> <https://www.google.com/maps/search/Prumyslova+595?entry=gmail&source=g> >> 252 50 Vestec near Prague >> Czech Republic >> >> Tel. +420 325 873 758 >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
