Hi again Ian, I will send the files to you in a private e-mail.
Best regards Kristoffer From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Ian Tickle <ianj...@gmail.com> Reply to: Ian Tickle <ianj...@gmail.com> Date: Wednesday, 12 October 2022 at 14:06 To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Error while running EDSTATS 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 <kristoffer.lundg...@teokem.lu.se<mailto:kristoffer.lundg...@teokem.lu.se>> wrote: Hi Ian, Thanks for looking into this! The -noerror flag seems to allow edstats.pl<http://edstats.pl> to run to completion for me as well. The maps for edstats.pl<http://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<http://edstats.pl> -xyzin bindividual1_fixed_refine_001.pdb -hklin hkl_ed.mtz -flabel FOBS -atomsf atomsf_neutron Best regards Kristoffer From: Ian Tickle <ianj...@gmail.com<mailto:ianj...@gmail.com>> Date: Tuesday, 11 October 2022 at 19:33 To: Kristoffer Lundgren <kristoffer.lundg...@teokem.lu.se<mailto:kristoffer.lundg...@teokem.lu.se>> Cc: "CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>" <CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>> 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 <00008a31f470d88b-dmarc-requ...@jiscmail.ac.uk<mailto:00008a31f470d88b-dmarc-requ...@jiscmail.ac.uk>> 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 ######################################################################## 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/
