On 18/02/15 23:31, Tc Cheng wrote:
Hi all,
Hi Tc, Happy goats?
I am currently using coot 0.8.2 pre-release on Centos 5.
good for you!
I have a ~ 4.4A EM map
OK! Not bad!
(in mrc format) that I want to build a model in coot.
OK!
The map shows up properly in chimera but not in coot.
<Sadness...>
In coot, it seems the map shows up multiple times at some regular grid points within the map radius,
I take this to mean that there are several blobs?
when dynamic map sampling and dynamic map display size clicked, without clicking these 2, nothing shows up.
Ah, I see... I think I need to improve how coot displays an EM map - Chimera does it better. Let's make that a new feature of 0.8.2!
(Chimera is amazingly fast at rotating EM maps.)
However, the maps that I downloaded from EMDB show up properly and fit right into their models in coot.
Glad to hear that.
I notice the EMDB maps are in CCP4 format (.map) but I wonder is there a major difference in .mrc vs .map format to cause this problem?
No, they are the same thing (unless they've been chomped on by an very old/broken version of Chimera).
as I suppose they are pretty similar.
Quite so.
I tried xmipp to convert the format from mrc to map,
In GNU, we'd us the "cp" command - haha!
but it doesn't work either.
Hmm... You mean that it fails in the same way, I take it?
And Is there any important information in the header that I should check or correct for? Any suggestion would be much appreciated.
At a guess, I think that it's simply a matter of looking at the right place in the map.
It should be straightforward for me to adjust coot's centring and sampling on reading an EM map. Maybe I'll do it as I cross the Atlantic tomorrow :-).
we can pursue this off-list if you like. Paul.
