Hmm….this is all a mess.
If the objective is that the users can generate the EXACT map the depositor saw, I agree, the output of the Refmac mtz file with the map coefficients would be good. Alas, no can do, because the Fs are not the same as in the input file, if I am understanding this correctly – reportedly Refmac does something (which is?) to them before it dumps them into the output mtz. So I deposit the SA file xyz-staraniso-merged-aniso _free.mtz to get closer to the data I used to input into refmac. Bad boy: (a) no can do, PDB no eat SA_flag. Maybe because the FreeR_flag is added as a second data set to the xyz-staraniso-merged-aniso.mtz. Ok, fixable. (b) no should do, because we actually want unmerged untruncated and unalterted I(obs) – which I agree - and with the XDS_whatever.HKL as close as I can get it. Seems we need a file description that includes all the desired items, and a little program the can harvest all that in a single cif file. As I put the ASCII XDS*.HKL file into StarAniso, there seems to be the perfect pre-processing site for all our desires. This SuperStar.mtz file then would additionally need only the map coefficients for the reflections actually used by Refmac to generate the map. Might well be that such does already exist as some sort of intermediate file. PDB_REPROCESS could take the unmerged HKL, process, and F-convert if desired, PDB_REDO could use these data then (or the I’s/F’s from SuperStar.mtz). I am sure this does not cover every conceivable combination, but it’s worth a discussion. Not that it could ever move through glacial committees…. In any case, I provide a link to the images for REDO_THE_DARN_JOB_YOURSELF. Cheers, BR PS: About the deposition read errors on mmcif files later. From: Ian Tickle <[email protected]> Sent: Monday, July 15, 2019 3:00 PM To: [email protected] Cc: [email protected] Subject: Re: [ccp4bb] SA_flag vs PDB Hi Bernhard Oh dear, yes that's quite possible. But in any case we recommend _not_ to deposit the output from STARANISO: http://staraniso.globalphasing.org/deposition_about.html Cheers -- Ian Cheers -- Ian On Mon, 15 Jul 2019 at 22:40, Bernhard Rupp <[email protected] <mailto:[email protected]> > wrote: Hi Fellows – wondering if there is a particular reason the PDB cannot process a mtz file that in addition to FreeR_flag includes a SA_Flag column from StarAniso? Can there be no more than one I column type because that is automatically interpreted as the free flag?? Best, BR ------------------------------------------------------ Bernhard Rupp Crystallographiae Vindicis Militum Ordo <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:[email protected]> [email protected] +1 925 209 7429 +43 676 571 0536 ------------------------------------------------------ Many plausible ideas vanish at the presence of thought ------------------------------------------------------ _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
