[Chimera-users] Doubt regarding cryeom map density threshold setting

Tom Goddard goddard at sonic.net
Tue Jul 24 10:19:42 PDT 2012

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 at sonic.net 
> <mailto:goddard at 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

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