Structure is not fitted and map has multiple duplicates in Coot
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.
Hi Ahmad, Coot may do some symmetry operations to show additional copies, but you’d have to ask the Coot people about it since we don’t know the details of that program. Saving a map in Chimera does not save any rotations that were applied, since the map format does not have anywhere to put that information. This is a commonly asked question in Chimera. Either you have to fit structures to map and then just save the atomic structures (PDBs) in the fitted positions, or if you want the density to be rotated you have to resample the map on a new grid with “vop resample” and then save the resampled map. See the help section “Saving Maps after Fitting," which has additional links for more details: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 20, 2019, at 12:46 PM, Ahmad Khalifa <underoath006@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>
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@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@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Ahmad Khalifa -
Elaine Meng -
Tom Goddard