[Chimera-users] Structure is not fitted and map has multiple duplicates in Coot

[Tom Goddard]

Hi Ahmad,

  As Elaine says, Coot is clearly applying crystallographic symmetry operations to your map.  Since Coot was written for x-ray crystallography maps that is not too surprising.  I don't think this has anything to do with volume eraser.  Maybe your PDB model has a CRYST1 record that gives a space group and unit cell parameters if it came from an x-ray structure determination, and maybe Coot is using that -- if so you might want to delete that CRYST1 from your PDB file.  MRC files also have a space group field in the header.  MRC files written by Chimera set the space group number to 0, indicating no space group or unknown.

	Tom


> On Mar 20, 2019, at 12:46 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> 
> I have a cryo-EM map that I want to segment. I have structures surrounding the density of interest from all sides. I did a molmap in chimera and subtracted everything the molmap. I then cleaned the excess density around my protein using volume eraser. 
> 
>  Now the map that I get opens fine in Chimera. But I tried to open a model and my density in Coot, the screenshot is what I got:
> 
> 1) the structure is not fitted
> 2) the density appears to have multiple copies of my proteins, it's supposed to be only one unit there
> 
> What is wrong here exactly, I'm suspecting it's the volume eraser! Is there a better way to segment the density given how I have atomic models for all the surrounding densities, but not the density of interest? 
> 
> Regards. 
> <coot_duplicates.PNG>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users