Thank you very much. I am trying to build a whole C15 model because I usually undergo refinement in Phenix after a round of fitting in Coot. What I have done so far was do one chain, copy and superpose, then use this model and my map for real space refinement. I guess the problem is that the map coordinates are not exactly correct.
Noha On Mon, Jul 1, 2024 at 7:20 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > On 7/1/24 12:24, Noha Elhosseiny wrote: > > Thanks Paul, > > I replied below in a different color > > On Mon, Jul 1, 2024 at 2:17 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> > wrote: > >> >> On 01/07/2024 11:59, Noha Elhosseiny wrote: >> > >> > >> > -- >> > >> > >> > >> > I am new to coot and structural analysis in general. I am trying to do >> > model building for a symmetric protein consisting of 15 identical >> > chains, using the density map from cryoEM analysis. I made an initial >> > model by first fitting one chain (chain A- roughly) in Chimera, copied >> > this chain to make the 15-mer, and then moved to coot for refinement >> > and improving the fitting. I noticed that there is a slight shift from >> > the best fit of the chain I fitted and then copied (chain A) in the >> > other chains in the density map. To cut it short chain A is perfect, >> > but chains B-O gradually shift very slightly from the ideal fit, >> > probably as a result of the copying process. Now I am not sure what to >> > do. I can try to work on each chain individually to fall into the >> > density like I did with chain A, but it seems counterintuitive to do >> > this 14 times when I already have a perfect chain.... I considered >> > doing LSQ superpose of chain A on each of the other chains, but given >> > they are already shifted...I think this will not solve the problem. I >> > also think I can try to do "refine chain" or "jiggle fit", but I think >> > this will make it worse not better as the chains are very slightly >> > shifted..... >> > >> > Any suggestions on how to proceed? >> > >> >> Presumably you have the transposition matrices from your cryo-EM >> processing. I imagine that it might even be proper symmetry. You can use >> that. What molecular symmetry do you have? >> > > I suppose I have...but I do not know how to get these matrices or where to > look for them....I am using CryoSPARC. I can look into where to get them. I > have a C15 symmetry and I am 90% sure it is correct as the protein is not > new but the species is and there are sequence differences..... > > > One generally modifies only one copy. When refining, one might make a > molecule of 5 chains (to model the interaction between chains) and then > modify only the middle (C) chain. > > You only need do the full symmetry expansion for deposition and making > figures. > > Attached is a script to do what you want (as far as I can tell) - you will > need to change the imol file and the centre to be appropriate for your > molecule. > > > Paul. > > > -- *Noha M. Elhosseiny, PhD* Department of Microbiology & Immunology Faculty of Pharmacy, Cairo University. Kasr El-Ainy St, Cairo, Egypt, 11562- Lab C-407 Website: https://eg.linkedin.com/in/nohaelhosseiny <https://eg.linkedin.com/in/nohaelhosseiny> ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
