Hi Sam, ARP/wARP should work well at 1.9A resolution. If it did not then there are things to check such as whether the space group is correct and whether there are major deviations in the Wilson plot.
Do you have a suspected sequence for chain B? If so, I would provide that to the programs to help them build. Once the backbone has been built you could trim it back to polyalanine in Coot and then use findMySequence. If you want to try a different model-building program I would try ModelCraft via CCP4i2 or CCP4 Cloud (but I may be biased). If you do this I would recommend providing both sequences (even if you just put polyalanine for chain B) and the correct number of copies so that density modification has more chance of improving the density for chain B. Kind regards, Paul On Sat, 4 Nov 2023, 14:04 Sam Tang, <samtys0...@gmail.com> wrote: > 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/
