What Oleg says is right. The phases may be too poor to Bootstrap from. Oleg also reminded me that the MR solution may be incorrect. I would check the following:
What were the TFZ and LLK scores for the MR solution (if you used Phaser for MR)? What are the R-factors after molecular replacement? Do they improve with 200 cycles of jelly-body refinement with Refmac (from the placed but unrefined model). How does the map look? Can you see clear difference density for where there are errors in the A chain, or any density for the B chain? If the A chain has no obvious errors try deleting a well-ordered residue and refine without it to look at the difference density. Kind regards, Paul On Sat, 4 Nov 2023, 14:16 Tsodikov, Oleg V., <oleg.tsodi...@uky.edu> wrote: > Sam, > > From what you wrote, it seems that the best thing is to build manually and > iteratively, at least at the beginning, starting with building the A chain > as well as you can and build parts of B as you go. MR phase has bias, of > course, so the only way is to do this is in many iterations. > I am assuming that chain B is relatively large, which is why your map > based on the structure of chain A alone (which itself may have errors) is > not great. In the end, you may have to get experimental phases, because the > MR phases may not be accurate enough to bootstrap from. > > Best wishes, > Oleg > > > > ------------------------------------------------------------------------- > Oleg Tsodikov, Ph.D. > Professor of Pharmaceutical Sciences > University of Kentucky College of Pharmacy > Todd Bldg, Room 425 > 789 S. Limestone St. > Lexington, KY 40536 > > phone: 859-218-1687 > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Sam Tang > <samtys0...@gmail.com> > *Sent:* Saturday, November 4, 2023 10:04 AM > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* [ccp4bb] About model building > > CAUTION: External Sender > > Dear community, > > I am solving the structure of a complex between proteins A and B, where A > is a protein with known homologs and B is a novel protein isolated from > plant. The diffraction data was at 1.9 Ang collected in-house, indexed to > P321. Using A as the search model, we have got a reasonable solution where, > after one round of refinement, the A chain fits the map pretty well. What's > left was to extend the termini and fit a few rotamers. > > For protein B (B chain) I have tried the web version of ARP/wARP but the > outcome was not really good. The model was not successfully built as > indicated by low model completeness and score. The tricky thing may be that > we do not have the complete sequence information of this protein B in-hand. > (The other way round, we more or less wish to rely on the high resolution > data to confirm its sequence.) What approach would you then recommend to > build the B chain in this scenario? > > Thanks in advance and best regards, > > Sam > > ------------------------------ > > 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/
