[Chimera-users] maintain .seg alignment to .mrc between sessions

Amy Jobe abj2111 at columbia.edu
Wed Mar 23 13:16:55 PDT 2016


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 at 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 at 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 at columbia.edu
Lab website:  http://franklab.cpmc.columbia.edu/franklab/
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