There is something seriously up the spout! Your Wilson plot gives an overall B factor of -5! Never seen that before! I am enquiring how that can happen... Eleanor
On Wed, 28 May 2025 at 15:11, Marius Schmidt <smar...@uwm.edu> wrote: > I think this might help, although I am not sure, really: > It might be worthwhile to try > k, h, -l as twin operator. Does not cost anything > since you figured it out in phenix anyway. Please let me > know whether this worked. > > Best > Marius > > Marius Schmidt, Dr. rer. Nat. (habil.) > Professor > University of Wisconsin-Milwaukee > Kenwood Interdisciplinary Research Complex > Physics Department, Room 3087 > 3135 North Maryland Avenue > Milwaukee, Wi 53211 > phone (office): 1-414-229-4338 > phone (lab): 414-229-3946 > email: smar...@uwm.edu > https://uwm.edu/physics/people/schmidt-marius/ > https://sites.uwm.edu/smarius/ > https://www.bioxfel.org/ > Nature News and Views: https://www.nature.com/articles/d41586-023-00504-4 > > > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Janani > Ganesh <jganesh3...@gmail.com> > *Sent:* Wednesday, May 28, 2025 6:22 AM > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* Re: [ccp4bb] Requesting help with twin refinement > > Dear Professor, > > Thank you for reviewing my data. Following your guidance, I have > reprocessed the dataset using XDS in P32 (No. 150) space group. After > completing integration, I proceeded with scaling and merging using AIMLESS. > > I have attached the AIMLESS log file for your review. > > I sincerely appreciate your continued support and valuable insights. > > Regards, > Janani Ganesh > > > On Wed, 28 May 2025 10:47:56 +0100, Eleanor Dodson < > eleanor.dod...@york.ac.uk> wrote: > > >WEll - I think this explains your crazy B values - you have somehow > >*normalised* the data at processing stagr. > >From the pointless log.. > >You usually dont need a reference data set and certainly not a set of > >calculated structure factors. > >Do you have CCP4I2 installed? > >If so just feed the integrated data through the processing and send me the > >log perhaps? > >.... > >*Reference list generated by structure factor calculation* > > from coordinate file > > >/home/janani-ganesh/Documents/JG/XData/K232Q_24042025_P72A5/CCP4I/K232Q_P72_phaser.1_refmac1.pdb > >Spacegroup: P 32 2 1 > >Cell: 81.84 81.84 134.77 90.00 90.00 120.00 > >Maximum resolution used: 1.884 > >Number of reflections: 42901 > >I*ntensity normalisation: B-factor = -8.7* > > > >*And taken from the phenix log:* > >Note that the <Fobs> at low resolution is slightly LOWER than at the > >highest resolution! This is unlikely. for a protein! > >..... > >F_model = k_total * (F_calc + k_mask * F_mask) > > > > k_total = k_isotropic * k_anisotropic > > Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani > >kmask > > 38.004-13.464 66.21 90 6 0.5449 232.778 190.690 0.824 0.739 > >0.353 > > 13.427-11.087 93.58 99 3 0.1952 *459.972 428.082 *1.279 > 0.749 > >0.340 > > 11.084-9.179 91.06 153 10 0.1983 502.739 469.985 1.271 0.749 > >0.330 > > 9.142-7.564 88.75 271 13 0.2210 405.976 376.935 1.215 0.751 > >0.329 > > 7.548-6.244 92.16 492 25 0.2733 342.193 302.079 1.212 0.751 > >0.328 > > 6.239-5.156 97.23 895 51 0.2545 365.657 321.767 1.164 0.750 > >0.321 > > 5.153-4.256 97.19 1575 83 0.1988 487.348 449.464 1.271 0.749 > >0.270 > > 4.256-3.514 99.83 2815 149 0.2169 582.502 526.163 1.702 0.748 > >0.084 > > 3.514-2.902 99.89 4989 263 0.2427 597.717 534.626 2.337 0.747 > >0.060 > > 2.901-2.396 99.85 8718 460 0.2988 532.605 456.384 2.752 0.744 > >0.000 > > 2.396-2.103 97.60 9284 494 0.3208 *546.159 458.454* 3.232 > 0.742 > >0.000 > > > >So fix your data processing first - then your B factors should become > >sensible and the R factors also - you are overweighting the high > resolution > >data greatly > > > > > >And if the crystal is twinned the space group is actually P 32.. > > > >Cheers Eleanor > > > > > > > >On Wed, 28 May 2025 at 08:04, Janani Ganesh <jganesh3...@gmail.com> > wrote: > > > >> Dear Professor, > >> > >> Thank you for your response. I had tried out TLS as well to understand > the > >> trend, but it did not work. I am attaching the detwin and pointless log > >> files for your reference. > >> > >> I even set the B-factors to an arbitrary value of 30 and performed > >> refinement with overall B-factors, but there was no change in the > B-factors > >> at all. > >> Is it possible for you to look at my data and help me with this issue? > >> > >> > >> With my best regards, > >> Janani Ganesh > >> PhD Scholar, Protein Crystallography Section, > >> Homi Bhabha National Institute, > >> Mumbai, India. > >> Contact No: +91-22-25594062 / +91-7506237778 > >> > > > >######################################################################## > > > >To unsubscribe from the CCP4BB list, click the following link: > > > 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