On 07/10/2024 10:43, SERGIO BARATA GARCIA wrote:
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Hi Paul!
Paul Emsley <pems...@mrc-lmb.cam.ac.uk> escribió:
On 04/10/2024 09:24, SERGIO BARATA GARCIA wrote:
I am processing a dataset of CryoEM in RELION and now that I have a
post-process map I want to build a model (model building) by fitting
a PDB structure into this CryoEM Volume.
Sounds fun.
As far as I know, Coot can read and open .mrc files, and indeed the
program opens the volume.mrc file.
Yes.
However, I can´t visualize it at all. I have played with the contour
level with no success.
The map doesn't fully cover the molecule you mean?
I mean that I can´t see the molecule at all. No signal in the display
window
Are you looking in the right place?
Calculate -> Modules -> Cryo-EM
Cryo-EM -> Go to Map Molecule Middle.
Try this:
Edit -> Map Parameters -> Map Radius EM -> 111 -> Apply
EM people who like to display big maps may be better off without
active map dragging:
Edit -> Preferences -> Maps -> Dragged Map -> No.
Regarding the volume is quite big so I do not know if that could
affect:
(x,y,z,n)= 660 x 660 x 660 x 1 ; avg= 9.14429e-05 stddev=
0.000812699 minval= -0.00536398 maxval= 0.0143412; angpix = 2.075
Those are inconveniently small levels I would say. Probably better to
scale them up by a million or so. I imagine that relion has a tool to
do that (Coot does not (well, not conveniently)).
I have modified both Map Radius and Dragged map, however I do not see
difference.
Regarding to the levels, I have increased the level contouring to
1000000 but I still. There are new map values:
(x,y,z,n)= 660 x 660 x 660 x 1 ; avg= 9.14429e-05 stddev= 0.000812699
minval= -0.00536398 maxval= 0.0143412; angpix = 2.075
I don't see a difference.
Paul.
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