Dear Betul, Please process the diffraction data in P63 is you mean to refine the structure in that space group. ============================================= CHENGHUA SHAO, Ph.D. Scientific Software Developer, RCSB Protein Data Bank Assistant Research Professor, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4968 | E: [email protected] rcsb.org | iqb.rutgers.edu | facebook https://www.facebook.com/RCSBPDB | twitter https://twitter.com/buildmodels | PDB-Carbohydrate https://doi.org/10.1093/glycob/cwab039 On 7/1/26 16:17, Tom Peat via phenixbb wrote:

Hello Betul,

The data and structure should have the same space group. I'm not sure if the PDB would allow deposition if the two didn't match. I would spend a little time to figure out which space group your data are in- clearly there seems to be some ambiguity and then re-refine the model in the appropriate space group. Best of luck, Tom ________________________________ From:[email protected] Sent: Thursday, July 2, 2026 2:29 AM To:[email protected] Subject: [phenixbb] PDB deposition question: processed data in P6₃22, refined model in P6₃

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Hello everyone,



I have a question regarding PDB deposition.



The processed diffraction data are in P6₃22, while the refined structure is in P6₃. During PDB deposition, the validation server reports a completeness of only ~51% which appears to result from the difference in symmetry between the processed data and the refined model.



Would it be acceptable to deposit the structure in this situation, or should the diffraction data be reprocessed in P6₃ and refined again before deposition?



Thank you very much for your advice!

Best, Betul _______________________________________________ phenixbb mailing list [email protected] To unsubscribe send an email [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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Dear Betul, If you still have the INTEGRATE.HKL file you could do that yes. XDS_ASCII.HKL are already scaled (and D1_1_xds.mtz is probably the same in MTZ format). You could do something like gemmi xds2mtz INTEGRATE.HKL INTEGRATE.mtz (see "gemmi xds2mtz -h" for additional arguments regarding polarisation and overloads - which you get from your XDS.INP file). The you can use AIMLESS for scaling etc. Remember that you should avoid running CORRECT (creating XDS_ASCII.HKL) followed by a AIMLESS scaling run: this is combining very different scaling algorithms on top of each other and it is better to stay in one system (i.e. XDS/CORRECT followed by XDSCONV or INTEGRATE.HKL/mtz -> AIMLESS). As you can see, there are several subtle and specific points that one has to look out for when doing the scaling+merging "right" - so by far the best is to get hold of the raw diffraction images and start again from there. In general: *always* keep the raw diffraction images ... as the name says: these are your raw data everything else derives from ;-) Cheers Clemens On Mon, Jul 13, 2026 at 05:27:56PM -0000, Betul wrote:

Dear Tom Peat, Chenghua Shao, Clemens Vonrhein, Nicholas Noinaj, and everyone,

Thank you all very much for your helpful advice and for taking the time to respond. I really appreciate your guidance. Based on your suggestions, I understand that the correct approach is to reprocess the diffraction data in P 63 and then carry out the final refinement in that space group.

Unfortunately, I do not currently have access to the raw diffraction images. At the moment, I only have the processed files generated during data processing (MTZ, HKL, log, and related files), which are listed below.

CORRECT.lp XDS_SCALE.hkl XSCALE (1).lp D1_1_xds.mtz (unmerged) D1_1_xds.log D1_1_aimless.mtz D1_1_aimless.log D1_1_truncate.mtz D1_1_truncate.log D1_1_pointless.log

Would it be possible to perform any re-scaling or other processing in Phenix (or another program) using only these files? Thank you again for your time and for sharing your expertise. Your explanations have been extremely helpful in understanding the source of the problem.

Best regards, Betul _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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