Automatic setting of suggested contour level
Hi Chimera team, I love how Chimera seems to intelligently and automatically choose a contour level for fetched EMDB files. However, I have noticed that most EMDB files have a "suggested contour level" associated with them. It can be obtained in the "header" XML files under the tag <contourLevel>. How much more work would it be to automatically fetch this information when fetching the map and then set the contour level to the recommended setting? Would you consider doing it? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
Hi Darrell, Chimera could fetch the EMDB XML metadata file and extract the suggested contour level and use it. I have noticed that the suggested levels are sometimes very wrong, deep in the noise. Some investigation will be needed to see if the levels are right often enough to be usable. I've made a Chimera feature request entry in our database. http://plato.cgl.ucsf.edu/trac/chimera/ticket/12644 It would be a good feature for Chimera 2 which we are working on but is probably a year or more away. I'm spending most time on our next generation Chimera 2 rather than adding features to the current Chimera 1. Tom On Nov 27, 2013, at 11:51 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote:
Hi Chimera team,
I love how Chimera seems to intelligently and automatically choose a contour level for fetched EMDB files. However, I have noticed that most EMDB files have a "suggested contour level" associated with them. It can be obtained in the "header" XML files under the tag <contourLevel>. How much more work would it be to automatically fetch this information when fetching the map and then set the contour level to the recommended setting? Would you consider doing it?
Thanks, Darrell
-- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
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Hi Tom, That certainly makes sense. I appreciate all your efforts in my behalf! Happy Thanksgiving, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559Web: BCBB Home Page <http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb .aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit <https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. On 11/27/13 5:01 PM, "Tom Goddard" <goddard@sonic.net> wrote:
Hi Darrell,
Chimera could fetch the EMDB XML metadata file and extract the suggested contour level and use it. I have noticed that the suggested levels are sometimes very wrong, deep in the noise. Some investigation will be needed to see if the levels are right often enough to be usable. I've made a Chimera feature request entry in our database.
http://plato.cgl.ucsf.edu/trac/chimera/ticket/12644
It would be a good feature for Chimera 2 which we are working on but is probably a year or more away. I'm spending most time on our next generation Chimera 2 rather than adding features to the current Chimera 1.
Tom
On Nov 27, 2013, at 11:51 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote:
Hi Chimera team,
I love how Chimera seems to intelligently and automatically choose a contour level for fetched EMDB files. However, I have noticed that most EMDB files have a "suggested contour level" associated with them. It can be obtained in the "header" XML files under the tag <contourLevel>. How much more work would it be to automatically fetch this information when fetching the map and then set the contour level to the recommended setting? Would you consider doing it?
Thanks, Darrell
-- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Page s/bcbb.aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
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participants (2)
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Hurt, Darrell (NIH/NIAID) [E] -
Tom Goddard