Hi Rakesh,

Chimera is not able to compute the local resolution of an EM map. Giovanni Cardone at the NIH has made a Chimera plug-in that does this and he talked about it at the 2011 3DEM Gordon conference. I don't know whether he ever distributed it. You should ask him.

Also Chimera does not have any method for computing local cross-correlation between a PDB model and a map. That would be nice. Is there a journal article evaluating a specific method for doing that?

For your Chimera internet connection problem it would help to know what Chimera web service you are trying to use. Are you fetching a PDB model? building a homology model? running BLAST? getting Uniprot annotations? Chimera has lots of web services

Hi,

I want to know how to color the cryoem map according to the local resolution and also according to the local cross correlation of the pdb structure with the map.

Moreover I am unable to connect to the internet in chimera inspite of providing the proxy address and port, how should I give the user name and password for authentication to connect inside chimera since I get authentication error.

Regards
Rakesh
On 7 July 2012 03:48, Tom Goddard <goddard@sonic.net> wrote:
You can choose a map contour so it encloses the expected number of cubic Angstroms as described here:

http://www.cgl.ucsf.edu/chimera/data/tutorials/eman07/chimera-eman-2007.html#part2

Tom
Hello,

My name is Rakesh. I would like to know how to set the density threshold according to the molecular mass of the protein in the cryoem map. I would also like to know how to calculate the molecular mass of a particular segment after segmentation in cryoem map.
Regards
Rakesh Ramachandran
PhD Student
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore - 560012
India