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 <[email protected]> on behalf of Sam Tang <[email protected]> Sent: Saturday, November 4, 2023 10:04 AM To: [email protected] <[email protected]> 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 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/
