Surely in this day and age, one would just run AF2? - it’s clearly the best homology modelling program ever, finding homologies that other programs can’t reach. I would - we are - using it to supply another “best guess” for difficult-to-build structures. One could even use it as an input for MR and hope.
Adrian On 6 Oct 2022, at 17:24, Schreuder, Herman /DE <herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> wrote: Dear Shawn, I am not aware of an automated way to merge all fragments into a single consistent peptide chain. What I would do is to look at the map and the built fragments in coot and switch the symmetry on with a large radius, e.g. 20-30A and see if you can find a set of fragments (including symmetry mates) that could form a complete and consistent protein molecule. If there is a suitable MR model available, I would try to match the fragments to the model (find equivalent amino acids). You could use the matching residues to superimpose the MR model e.g. onto the largest fragment available. The next step would be to rebuild the MR model using the electron density map and the built fragments as a guide. If there is no suitable MR model, I would probably built the whole protein, starting from the largest fragment, using the built residues as a guide. For this you can use the “add residue” option and put the residue created at the position of the equivalent residue of a fragment. Every 3-5 residues, you should do a real space refinement. The pdb standard accepts negative residue numbers, so you should be able to build in N-terminal direction as well. Afterwards you will have to renumber the protein to get the correct numbering. The alternative would be to select the correct symmetry mate for each fragment, write them out, renumber them and merge them into a single pdb file. However, in my experience, this is much more hassle than the build them “from scratch” as I mentioned. Good luck, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Im Auftrag von Shawn Rumrill Gesendet: Mittwoch, 5. Oktober 2022 22:42 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: [ccp4bb] Fragmented Chains after Automated Rebuilding Hello All, I am trying to solve a protein/nucleic acid (na) structure. The density for na is poor and MR is less straightforward, so I used ModelCraft for automated phasing, rebuilding and improving the electron density. It has built a partial model for the complex, which looks somewhat reasonable, however, the protein and na chains are fragmented, which throws off numbering, etc. I'm sure this is expected, but I typically don't do automated rebuilding (necessary in this case). Is there any way to easily connect and renumber the chains and residues (perhaps using a reference PDB structure) to try and build something more complete (in terms of chains and residues)? I have not worked with a protein/na complex so certainly na modeling is new to me. Any input is greatly appreciated! Thanks for your expertise, Shawn ######################################################################## 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/<https://www.jiscmail.ac.uk/policyandsecurity> ________________________________ 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/
