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]
<mailto:[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.
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