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/
