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/
