Dear Paul, Thank you very much for your response. I apologize for my late reply. I am working on trying to find the correct map coordinates to be able to run the script. I am grateful for your time and I am sorry if my questions and responses are rather stupid. I am very new to this and I am trying to learn, so thanks a lot indeed.
Noha On Tue, Jul 2, 2024 at 4:00 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > On 02/07/2024 13:17, Noha Elhosseiny wrote: > > > -- > 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. >> > > > I am trying to build a whole C15 model because I usually undergo > refinement in Phenix after a round of fitting in Coot > > So, do you think you need a whole C15 model to refine in Phenix? > > I doubt that that is the case (I mean, I would be very surprised if you > needed to do so). I imagine Phenix is able to refine a handful of monomers > just like Refmac or Coot can. > > > What I have done so far was do one chain, copy and superpose, then use > this model and my map for real space refinement. > > Sounds like quite some palaver. > > > I guess the problem is that the map coordinates are not exactly correct > > If you are using Coot, that is not a good place to start. > > Were you able to find the transformation matrix from the output of > CryoSPARC? > > Were you able to run the script to correctly produce your whole C15 > 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/
