Doubt regarding cryeom map density threshold setting
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
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... 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
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...
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
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 <mailto: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...
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
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 <mailto: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...
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
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: http://docs.python.org/library/urllib.html 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 http://stackoverflow.com/questions/34079/how-to-specify-an-authenticated-pro... I've made a Chimera bug database entry for this problem but think you will need to solve this outside of Chimera. http://plato.cgl.ucsf.edu/trac/chimera/ticket/11212 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. Tom -------- 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...
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
participants (2)
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rakesh ramachandram -
Tom Goddard