Hi Paul, Yes, I extract one single subunit just to quickly access the shape or the sequence of the ordered region; next I would like to model 3~5 subunits. The reason I think segmentation is necessary is, many subunits at the ends of the filament were half chopped off (by masking in relion). So, to have a map consisting of entirely full subunits, I tried to clean up the ends. However, even doing so ended up replicate display problems in Coot (just tested a "clean" 5mer in a 125*109*59 box). It seems that as long as I use segment->select->save selected region function in Segger, it will cause such problems. So I guess the question now is, how should one extract a subregion of a map without causing display problems in Coot? Any information/background/suggestion are welcome!
Best, Qiuye On Sun, Sep 20, 2020 at 10:41 PM Paul Emsley <[email protected]> wrote: > > On 20/09/2020 19:27, Qiuye Li wrote: > > > The protein is a filament and the reconstructed map is in a 512*512*512 > box. I segmented this reconstructed map in Chimera using Segger, selected a > single asymmetrical unit, and saved it as a new map (which was referred to > as the segmented map). This new map automatically changed to a box size of > 94*84*26. > > > That does seem a bit thin in z. Does segger know about helical symmetry? > If not, I don't think that this is a winning strategy. > > But it does occur to me to wonder why you even need to segment the map. > Relion tells you the helical symmetry and you should (it seems to me) just > apply that to the model. > > if you even need to do that... I would build a model into the set of tubes > in the middle, and then when I wanted to be concerned about symmetry, just > try cut paste rotate translate (just shove it up a rung and use jiggle fit) > and let the NCS chain copy tool modify the other chains as I go. From what > I can see of your map, one chain either side of the central chain should be > enough. > > > Paul. > > > BTW, I tried to display from another direction and it looks like these > copies do lie along the axis, see the attachment. > > Best, > Qiuye > > > On Sun, Sep 20, 2020 at 1:29 PM Paul Emsley <[email protected]> > wrote: > >> >> On 20/09/2020 17:29, Qiuye Li wrote: >> > >> > Thanks for the suggestion, it looks map segmentation and coot do not >> > work well with each other, see the tests I did below: >> > >> > 1. .mrc map directly from relion: >> > in Chimera: OK >> > in Coot: OK >> > >> > 2. segmented map generated from Chimera: >> >> >> what do you mean by "segmented"? >> >> >> > in Chimera: OK >> > in Coot: displayed as replicates >> > >> > When I segment the map, the box dimensions and map threshold level >> > were changed, would these cause problems? >> > >> >> I am not really sure what you mean by the map threshold level. It's >> something of a surprise that the box (cell) dimensions have changed. >> Maybe that's a result of reboxing? But I doubt that that would cause >> problems to Coot. >> >> >> It looks like the map is interspersed with sections that have zero >> value. However, from the orientation axes top left it doesn't seem that >> the sections lie along the direction of a cell axis. >> >> >> Paul. >> >> >> ######################################################################## 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/
