Vera, I had a similar case and I solved it using the PDB tool pdb_extract from: https://pdb-extract.wwpdb.org/ PDB Extract is a pre-deposition service for assembling structure files for wwPDB OneDep deposition .
You have a pdb and you have a mtz file, then you should be able to convert them to the latest mmcif format. After that you can deposit your files in: https://deposit-1.wwpdb.org/deposition/ https://validate-rcsb-2.wwpdb.org/ Since you used anisotropic data and different software, the final R/Rfree will likely be different of the estimated during PDB validation, and you will have the opportunity to explain it to the person from the PDB that will help you during your deposition. Finally, if you are using PHENIX, BUSTER, REFMAC/CCP4, you can also run a last refinement step with the latest version of the software. The latest version will ensure that the mmcif format is compatible with the PDB. Sometimes older versions of the software will give you that type of error. Good luck, Joao From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Vera Pfanzagl Sent: Monday, July 11, 2022 10:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] [ccp4bb] problems in Rfree-flags when refining with REFMAC and processing with STARANISO 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<https://urldefense.com/v3/__https:/staraniso.globalphasing.org/test_set_flags_about.html__;!!H9nueQsQ!_IB8G3WAOxxFQn5h4jDFwAmN1RVYVhI2LKrKWB5_94y6bVx9BkPLOZgonHnWVltzEZXXeqtezxw6x39nT1tLrXv_1w$> to generate a staraniso_mtz suitable for refinement in REFMAC, phased it again with my initial model and ran a refinement cycle, because I thought skipping a program might be a good idea. However I do not know if the mtz file I get has the appropriate column labels and also I do not know how to convert it to an mmcif that includes the data from processing. i have never before tried to combine AUTOPROC-processed data with REFMAC data and am not very familiar with REFMAC to begin with. I have tried the sftool server to validate the mtz from REFMAC processing but I get an error message Converting SF file to mmcif format ... Warning: (data block=1): all status (80493) are assigned as 'x' (changed! 'x'->'o') Error: File (xxxx) has no mandatory items 'F/I/F+/F-/I+/I-' (data block=1) I tried to use Phenix (as it automatically converts the mtz to an mmcif file) by running a "mock"-refinement with fixed coordinates but the mmcif file I get out of this seems to contain some wrongly labeled data fields in block 1 when I try to upload it to PDBs validation server. Essentially it seems to contain some 30000 data points in block 1 that have a ? This is the error message I receive: Warning: (data block=1): 30301 reflections have status assigned as '?' (changed to 'x') Warning: (data block=1): 30301 reflections have wrong status. Not in list(o,f,x,-,<,h,l) Warning: No wavelength value was found in SF file (data block=1). which is essentially the same as above, so I guess it is derived from the same problem. I would be very grateful for any help. Cheers and thanks, Vera ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!H9nueQsQ!_IB8G3WAOxxFQn5h4jDFwAmN1RVYVhI2LKrKWB5_94y6bVx9BkPLOZgonHnWVltzEZXXeqtezxw6x39nT1tvNXKb7A$> ######################################################################## 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/
