maintain .seg alignment to .mrc between sessions
Hello, When I segment an 80S ribosome into individual ribosomal proteins and rRNAs, it takes some time and I often need to close and reopen my session. Whenever I reopen my session, though, my .seg file is no longer aligned to my .mrc map, and I have to spend time manually (and probably slightly inaccurately) re-aligning them. I've tried using the Associate Selected option in the daily build, although I'm not sure if it's meant to maintain alignment, and it hasn't fixed the problem. Can anyone help me with this? I'm using the daily build and the most recent stable version on Mac. Thanks, Amy Jobe -- PhD candidate, Joachim Frank group Department of Biological Sciences Columbia University 2-221 P & S Black Building 650 W. 168th St. New York, NY 10032 Telephone: (315) 879-8192 E-mail: abj2111@columbia.edu Lab website: http://franklab.cpmc.columbia.edu/franklab/
Hi Amy, I tried to reproduce this in simple tests but I didn’t have the problem. Although (at least in my tests) the segmentation surfaces weren't restored automatically with the session, if I’d previously used “save segmentation” to save the segmentation to a file, I could just reopen it from the Segment Map menu and it was aligned properly with the map. My only idea, however, is that perhaps the data set was moved separately at some point. It may be possible to bring them back into register by (A) copying the transformation of the map model to the segmentation model, e.g. matrixcopy #N #M … where N is the model number of the map and M is the model number of the segmentation (see model numbers by showing the Model Panel from the Favorites menu). or (B) by resetting all model positions, e.g. command: reset If neither of those work, we may need to seek other opinions. Our expert on staff is away for a couple of weeks, but others may have something to add. Best, 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 Mar 23, 2016, at 10:30 AM, Amy Jobe <abj2111@columbia.edu> wrote:
Hello, When I segment an 80S ribosome into individual ribosomal proteins and rRNAs, it takes some time and I often need to close and reopen my session. Whenever I reopen my session, though, my .seg file is no longer aligned to my .mrc map, and I have to spend time manually (and probably slightly inaccurately) re-aligning them. I've tried using the Associate Selected option in the daily build, although I'm not sure if it's meant to maintain alignment, and it hasn't fixed the problem. Can anyone help me with this? I'm using the daily build and the most recent stable version on Mac.
Thanks, Amy Jobe
Hi Elaine and users, The matrixcopy #map #segmentation tip worked; thank you so much. I wasn't aware of this command before. Thank you, Amy Jobe On Wed, Mar 23, 2016 at 4:04 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Amy, I tried to reproduce this in simple tests but I didn’t have the problem. Although (at least in my tests) the segmentation surfaces weren't restored automatically with the session, if I’d previously used “save segmentation” to save the segmentation to a file, I could just reopen it from the Segment Map menu and it was aligned properly with the map.
My only idea, however, is that perhaps the data set was moved separately at some point. It may be possible to bring them back into register by (A) copying the transformation of the map model to the segmentation model, e.g.
matrixcopy #N #M
… where N is the model number of the map and M is the model number of the segmentation (see model numbers by showing the Model Panel from the Favorites menu).
or (B) by resetting all model positions, e.g. command:
reset
If neither of those work, we may need to seek other opinions. Our expert on staff is away for a couple of weeks, but others may have something to add. Best, 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 Mar 23, 2016, at 10:30 AM, Amy Jobe <abj2111@columbia.edu> wrote:
Hello, When I segment an 80S ribosome into individual ribosomal proteins and rRNAs, it takes some time and I often need to close and reopen my session. Whenever I reopen my session, though, my .seg file is no longer aligned to my .mrc map, and I have to spend time manually (and probably slightly inaccurately) re-aligning them. I've tried using the Associate Selected option in the daily build, although I'm not sure if it's meant to maintain alignment, and it hasn't fixed the problem. Can anyone help me with this? I'm using the daily build and the most recent stable version on Mac.
Thanks, Amy Jobe
-- PhD candidate, Joachim Frank group Department of Biological Sciences Columbia University 2-221 P & S Black Building 650 W. 168th St. New York, NY 10032 Telephone: (315) 879-8192 E-mail: abj2111@columbia.edu Lab website: http://franklab.cpmc.columbia.edu/franklab/
participants (2)
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Amy Jobe -
Elaine Meng