AoA I am student of BS Bioinformatics & Biotechnology How to check or see the resolution of a model in Angstrom Chimera , kindly tell me
Chimera cannot figure out the resolution of a density map, and the density map file formats (CCP4, MRC, BRIX,….) do not specify the resolution in the file. You need to get that information from the researchers who calculated the map. For electron microscopy the resolution is usually calculated by computing two density maps each using half the experimental data and comparing the two maps. For X-ray crystallography the resolution is based on which diffraction spots were observed. If you want to find out the density map grid plane spacing use the Chimera Volume Viewer dialog menu entry Features / Coordinates and look at the Voxel Size value. This is not the resolution. Usually it is approximately 1/3 of the resolution. Tom On Apr 3, 2013, at 8:19 AM, Muhammad ALi wrote:
AoA
I am student of BS Bioinformatics & Biotechnology How to check or see the resolution of a model in Angstrom Chimera , kindly tell me
Hello, That information would come from the same source as the data, and it may just be easier to look at that source. In other words, you could go to the RCSB PDB website to check information on a PDB structure, or the EMDB website to check information on a density map from the EMDB. For links to those websites, see here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html> Chimera does not calculate resolution. If the source does not provide that information (for example, another scientist gave you a density map in progress), there isn't a way to guess it in Chimera. However: In Chimera, you can look up the resolution for a PDB structure if it was in the header of the PDB file. You would have to open the Model Panel (in menu under Favorites), choose that structure on the left, and then click "attributes..." on the right. Then, in the resulting attributes dialog, click the "PDB Headers..." button at the bottom to see the header information. Personally, I find it difficult to find "RESOLUTION" in all this information, so I usually just open the original PDB file in a text editor program (not in Chimera) and search for "RESOLUTION" or look at the RCSB PDB website, as mentioned above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 3, 2013, at 8:19 AM, Muhammad ALi wrote:
AoA I am student of BS Bioinformatics & Biotechnology How to check or see the resolution of a model in Angstrom Chimera , kindly tell me
very good... thank you sir --- On Wed, 4/3/13, Elaine Meng <meng@cgl.ucsf.edu> wrote: From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Resolution To: "Muhammad ALi" <muh.ali741@yahoo.com> Cc: chimera-users@cgl.ucsf.edu Date: Wednesday, April 3, 2013, 5:30 PM Hello, That information would come from the same source as the data, and it may just be easier to look at that source. In other words, you could go to the RCSB PDB website to check information on a PDB structure, or the EMDB website to check information on a density map from the EMDB. For links to those websites, see here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html> Chimera does not calculate resolution. If the source does not provide that information (for example, another scientist gave you a density map in progress), there isn't a way to guess it in Chimera. However: In Chimera, you can look up the resolution for a PDB structure if it was in the header of the PDB file. You would have to open the Model Panel (in menu under Favorites), choose that structure on the left, and then click "attributes..." on the right. Then, in the resulting attributes dialog, click the "PDB Headers..." button at the bottom to see the header information. Personally, I find it difficult to find "RESOLUTION" in all this information, so I usually just open the original PDB file in a text editor program (not in Chimera) and search for "RESOLUTION" or look at the RCSB PDB website, as mentioned above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 3, 2013, at 8:19 AM, Muhammad ALi wrote:
AoA I am student of BS Bioinformatics & Biotechnology How to check or see the resolution of a model in Angstrom Chimera , kindly tell me
You should be able to get that information from both the header of the pdb when opened as text, or from the rcsb.org website where the structures are archived. Rebecca Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768 On 4/3/2013 11:19 AM, Muhammad ALi wrote:
AoA
I am student of BS Bioinformatics & Biotechnology How to check or see the resolution of a model in Angstrom Chimera , kindly tell me
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participants (4)
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Elaine Meng -
Muhammad ALi -
Rebecca Swett -
Tom Goddard