Hi Joao Can you post the mtzdmp output?
Cheers Ian On Tue, 16 Jun 2020, 09:30 Joao Ramos, <jc.ra...@campus.fct.unl.pt> wrote: > Dear Ian, > > I'm trying to use the edstats.pl script but I'm having problems with the > column labels. mtzdmp can read the mtz file, but edstats.pl gives me a > message saying that mtzfix cannot find the labels. I'm using a mtz file > from a refinement job in Phenix. > > Best regards, > Joao Ramos > > Ian Tickle <ianj...@gmail.com> escreveu no dia terça, 16/06/2020 à(s) > 09:39: > >> Hi João >> >> In cases like this it's always a good idea to check whether you can read >> the same MTZ file with mtzdmp. If that fails with the same error message >> it means that the pathname/filename was indeed incorrectly specified, or it >> could possibly be a permissions issue (the file needs to be given read >> permission). >> >> Cheers >> >> Ian >> >> >> On Mon, 15 Jun 2020, 19:09 Ian Tickle, <ianj...@gmail.com> wrote: >> >>> >>> Hi Joao >>> >>> The top of the page was cut off in your screenshot so I can't see the >>> command line you typed. It would be better to copy/paste the entire text, >>> including the input command line and the output, into the email rather than >>> taking a screenshot. 'Cannot open file' most likely means that the input >>> filename was not typed correctly or the path was not specified correctly if >>> it's in another directory. Anyway you really shouldn't be calling the >>> MTZFIX or EDSTATS programs directly. Using the Perl script 'edstats.pl >>> ' http://www.ccp4.ac.uk/dist/checkout/edstats/edstats.pl is much >>> easier. It should be in your path after running the CCP4 setup script. >>> >>> Cheers >>> >>> -- Ian >>> >>> >>> On Mon, 15 Jun 2020 at 18:41, Joao Ramos <jc.ra...@campus.fct.unl.pt> >>> wrote: >>> >>>> Dear Ian, >>>> >>>> Thanks for the reply! >>>> >>>> I've sourced the setup script, but now I get a 'cannot open file' error >>>> message (screenshot attached) when trying to run MTZFIX. >>>> >>>> Best regards, >>>> Joao Ramos >>>> >>>> Ian Tickle <ianj...@gmail.com> escreveu no dia segunda, 15/06/2020 >>>> à(s) 16:57: >>>> >>>>> >>>>> Hi Joao >>>>> >>>>> For all CCP4 programs you need to source your CCP4 setup script. >>>>> >>>>> Cheers >>>>> >>>>> -- Ian >>>>> >>>>> >>>>> On Mon, 15 Jun 2020 at 15:29, Joao Ramos <jc.ra...@campus.fct.unl.pt> >>>>> wrote: >>>>> >>>>>> Dear CCP4bb, >>>>>> >>>>>> I'm trying to obtain RSC metrics using the CCP4 program EDSTATS for a >>>>>> Phenix refinement job, in order to have a more reliable analysis of model >>>>>> quality. From what I read, one should go through the program MTZFIX and >>>>>> then create the FFT maps (density and difference maps). However, while >>>>>> attempting to run the Phenix output mtz file in MTZFIX, I receive an >>>>>> error >>>>>> message saying: "Cannot open environ.def". >>>>>> >>>>>> My questions are: >>>>>> 1) Is the way to go from the Phenix refinement output files to >>>>>> EDSTATS described earlier correct? Are there alternative programs >>>>>> included >>>>>> in Phenix? >>>>>> 2) How to fix the error and run MTZFIX? >>>>>> >>>>>> I'm currently using the new ccp4 v7.1, in macOS v10.14.5. >>>>>> >>>>>> Best regards, >>>>>> Joao Ramos >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>>> https://www.jiscmail.ac.uk/cgi-bin/wa.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/
