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

Tom Goddard goddard at sonic.net
Tue Jul 24 12:17:50 PDT 2012

Hi Rakesh,

   The Chimera web proxy settings in Preferences / Web Access do not 
support proxy servers which require authentication.  Chimera is using 
the Python language urllib module http_proxy environment variable 
described here:


and it says if this variable is not used then the proxy settings are 
obtained on Windows from the registry's Internet Settings section.  You 
also might be able to set the http_proxy environment variable yourself 
including the user name and password as described at the bottom (Oct 15, 
2010) of this discussion


I've made a Chimera bug database entry for this problem but think you 
will need to solve this outside of Chimera.


   You can google for Giovanni and get  his email.  It was in the top 
hit searching for Giovanni Cardone NIH.

   Supplementary figure 5 of " GTPase activation of elongation factor 
EF-Tu by the ribosome during decoding", Schuette, et al. says "The local 
CCC was calculated within a moving box (size 9x9x9 pixels at 1.26 Å 
pixel size) in steps of 4 pixels. "  Although the figure caption says it 
was made with Chimera, that moving box calculation is not a Chimera 
capability and they must have written their own code or used someone 
else's code to do that and you would need to ask them.


-------- Original Message --------
Subject: Re: [Chimera-users] Doubt regarding cryeom map density 
threshold setting
From: rakesh ramachandram
To: Tom Goddard
Date: 7/24/12 11:26 AM
> Hi,
>  Thanks for the message. I tried the webservice without proxy but 
> unable to connect it. I was trying to fetch the pdb and for homology 
> modeling. Moreover the report a bug option is also not working since 
> it is unable to connect to internet.
>  Do you have the email id of Giovanni Cardone so that I can write to 
> him for the plugin. I recently saw its use in two papers.
> I saw a method in this article "GTPase activation of elongation factor 
> EF-Tu by the ribosome during decoding" in EMBO journal where for 
> generating supplementary figure 5 they have used chimera and colored 
> according to the cross correlation value with a threshold. I would be 
> grateful if you can explain me the methodology after you read it and 
> how to generate it in chimera.
> Regards
> Rakesh
> On 24 July 2012 22:51, Tom Goddard wrote:
>     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 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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