Hello,
I am trying to get a structure with a bit of a history in terms of programs I have used into a deposit-able form. However I have massif problems with the mtz labels, specifically the Rfree flags and cannot figure out where my problem is derived from. Specifically I have collected diffraction data on a very anistropic crystal (3 A in one direction and 1.4 in the other) which I processed using AUTOPROC because I wanted to make use of the inbuild STARANISO processing. I then went to Phenix for molecular replacement and refined a few rounds with Phenix. However one of my co-factors (a twice covalently linked heme) did not refine properly, which is why i switched the refinement to CCP4 and used REFMAC. What I initially did not know is that REFMAC and STARANISO do not go well together when it comes to the Rfree-flags in the diffraction cut-off regions. I went back and tried to use SFtools by CCP4 as described on https://staraniso.globalphasing.org/test_set_flags_about.html to generate a staraniso_mtz suitable for refinement in REFMAC, phased it again with my initial model and ran a refinement cycle, because I thought skipping a program might be a good idea. However I do not know if the mtz file I get has the appropriate column labels and also I do not know how to convert it to an mmcif that includes the data from processing. i have never before tried to combine AUTOPROC-processed data with REFMAC data and am not very familiar with REFMAC to begin with. I have tried the sftool server to validate the mtz from REFMAC processing but I get an error message Converting SF file to mmcif format ... Warning: (data block=1): all status (80493) are assigned as 'x' (changed! 'x'->'o') Error: File (xxxx) has no mandatory items 'F/I/F+/F-/I+/I-' (data block=1) I tried to use Phenix (as it automatically converts the mtz to an mmcif file) by running a "mock"-refinement with fixed coordinates but the mmcif file I get out of this seems to contain some wrongly labeled data fields in block 1 when I try to upload it to PDBs validation server. Essentially it seems to contain some 30000 data points in block 1 that have a ? This is the error message I receive: Warning: (data block=1): 30301 reflections have status assigned as '?' (changed to 'x') Warning: (data block=1): 30301 reflections have wrong status. Not in list(o,f,x,-,<,h,l) Warning: No wavelength value was found in SF file (data block=1). which is essentially the same as above, so I guess it is derived from the same problem. I would be very grateful for any help. Cheers and thanks, Vera ######################################################################## 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/
