Hi Kristoffer OK I see that the MTZ file you used going into EDSTATS (hkl_ed.mtz) does have an FOM column so I'm still puzzled why it didn't work the first time. Ignoring errors is only a good idea if you know what the errors are and are confident they're not going to affect the results! I would need this file to work out what exactly happened.
Cheers -- Ian On Wed, 12 Oct 2022 at 12:03, Kristoffer Lundgren < [email protected]> wrote: > Hi Ian, > > > > Thanks for looking into this! > > > > The -noerror flag seems to allow edstats.pl to run to completion for me > as well. > > > > The maps for edstats.pl are generated by using phenix.maps (version > 1.20.1-4487) with the attached maps.params file (maybe this file is > configured wrong?). Before this step I have run a quantum refinement of the > model as outlined in > https://onlinelibrary.wiley.com/iucr/doi/10.1107/S205979831900175X which > is the reason for the slightly changed file names. > > > > EDSTATS is then executed through a small script: > > > > cad hklin1 bindividual1_fixed_refine_001_fmodel.mtz hklin2 > bindividual1_fixed_refine_001_map_coeffs.mtz hklout hkl_ed.mtz<<EOF > > LABIN FILE 1 E1=FOBS E2=SIGFOBS E3=FCALC E4=PHIFCALC E5=FOM E6=R_FREE_FLAGS > > LABOUT FILE 1 E1=FOBS E2=SIGFOBS E3=FC E4=PHIC E5=FOM E6=FREE > > LABIN FILE 2 ALL > > EOF > > edstats.pl -xyzin bindividual1_fixed_refine_001.pdb -hklin hkl_ed.mtz > -flabel FOBS -atomsf atomsf_neutron > > > > Best regards > > Kristoffer > > > > > > *From: *Ian Tickle <[email protected]> > *Date: *Tuesday, 11 October 2022 at 19:33 > *To: *Kristoffer Lundgren <[email protected]> > *Cc: *"[email protected]" <[email protected]> > *Subject: *Re: [ccp4bb] Error while running EDSTATS > > > > > > Hi Kristoffer > > > > The deposited structure factor file is missing an FOM column which is > needed for MTZFIX to do its job of checking the veracity of the FWT and > DELFWT columns. The message I get with CCP4 7.1 is different, in fact it's > exactly what I expect: > > > > mtzfix: ERROR: Labels not found - maybe non-standard labels used? > > > > i.e. telling you that it's missing required column(s), not the "corrupt > output file" message which suggests something got mangled. > > > > Can you tell me _exactly_ what you typed on the command line from the > point after you downloaded and unzipped the data files? > > > > What happens if you skip the MTZFIX step by adding the '-noerror' flag to > the command line? This ran to completion for me, though I haven't checked > the results to see if they make sense. > > > > If that doesn't help you will have to recompute the structure factors from > the model using 'NCYC 0' in Refmac. That will output all the required > columns so you should be able to proceed normally. > > > > The error message "ERROR in radius calculation: max iterations" indicates > a more serious problem, such as an inability to handle the density profile > for Mn. I'm puzzled how it got that far since the MTZFIX failure should > have terminated the run before it got to that point. > > > > See if any of that helps. > > > > Cheers > > > > -- Ian > > > > > > On Tue, 11 Oct 2022 at 17:09, Kristoffer Lundgren < > [email protected]> wrote: > > Dear all, > > > > I am trying to run EDSTATS on a neutron structure containing a manganese > ion (https://www.rcsb.org/structure/7KKW), but either I am doing > something wrong or something is broken. When using EDSTATS supplied with > CCP4 8.0 I end up with the error message: > > > > mtzfix: WARNING: Output file is corrupt so deleted. > > > > ERROR in mtzfix: stopping. > > > > > > Using EDSTATS supplied with CCP4 7.0, the error message instead becomes: > > > > ERROR in radius calculation: max iterations. > > > > ERROR in RADINT: 2 > > > > > > Oddly enough, when changing MN to FE in the model, EDSTATS in CCP4 7.0 > works fine. EDSTATS in CCP4 8.0 with FE however again gives me the error > message: > > > > mtzfix: WARNING: Output file is corrupt so deleted. > > > > ERROR in mtzfix: stopping. > > > > > > Any help or advice would be greatly appreciated! > > > > Kind regards > > Kristoffer Lundgren > > > ------------------------------ > > 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/
