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

    http://www.cgl.ucsf.edu/chimera/docs/webservices.html

and perhaps some do not use the proxy setting in Chimera / Preferences / Web Access.  You could use Chimera menu Help / Report a Bug... to get help on this problem -- probably better than using the mailing list.

    Tom



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