[Chimera-users] Doubt regarding cryeom map density threshold setting
goddard at sonic.net
Tue Jul 24 10:21:39 PDT 2012
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
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.
> 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.
> 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:
>> 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.
>> Rakesh Ramachandran
>> PhD Student
>> Molecular Biophysics Unit,
>> Indian Institute of Science,
>> Bangalore - 560012
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