segmenting cryoEM maps
Dear all, I am new to chimera and I am working with density maps. I have segmented my cryoEM map successfully. I want now to group some of the segmented regions in a single region and subequently save the obtained map. Is there a way of doing it? Thank you very much Best wishes Giulia Palermo
Hi Giulia, If you are using the “Segment Map” tool in Chimera (in menu under Tools… Volume Data), it has many features for grouping the resulting segmentation regions and saving results. You can click the Help button to see the manual page included in your download, or see the copy on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html> There is more information including videos here: <http://ncmi.bcm.edu/ncmi/software/segger/docs> Segmentation produces surfaces, not a map, but I’m guessing you want to save the parts of the original map that fall within the surfaces (masking), and this can be done using the File menu in the Segment Map tool. 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 Aug 19, 2016, at 10:35 AM, giulia palermo <giulia.palermo83@gmail.com> wrote:
Dear all, I am new to chimera and I am working with density maps. I have segmented my cryoEM map successfully.
I want now to group some of the segmented regions in a single region and subequently save the obtained map.
Is there a way of doing it? Thank you very much
Best wishes Giulia Palermo
Dear Elaine, thank you for your reply. I did it! Chimera is a very useful tool. thank you again Giulia 2016-08-19 18:04 GMT-07:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi Giulia, If you are using the “Segment Map” tool in Chimera (in menu under Tools… Volume Data), it has many features for grouping the resulting segmentation regions and saving results. You can click the Help button to see the manual page included in your download, or see the copy on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html>
There is more information including videos here: <http://ncmi.bcm.edu/ncmi/software/segger/docs>
Segmentation produces surfaces, not a map, but I’m guessing you want to save the parts of the original map that fall within the surfaces (masking), and this can be done using the File menu in the Segment Map tool. 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 Aug 19, 2016, at 10:35 AM, giulia palermo <giulia.palermo83@gmail.com> wrote:
Dear all, I am new to chimera and I am working with density maps. I have segmented my cryoEM map successfully.
I want now to group some of the segmented regions in a single region and subequently save the obtained map.
Is there a way of doing it? Thank you very much
Best wishes Giulia Palermo
participants (2)
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Elaine Meng -
giulia palermo