[Chimera-users] saving a map after rotation

Li, Zongli Zongli_Li at hms.harvard.edu
Fri Jan 2 16:16:25 PST 2015

Thank you, Elaine!


From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Friday, January 02, 2015 5:05 PM
To: Li, Zongli
Cc: Mailing List
Subject: saving a map after rotation

Hi Zongli,
Happy new year!

The main issue is that the map file format doesn’t include rotation information.  If you rotated your map to go with some atomic structure (PDB file), it is better to save a new PDB relative to the map instead.  If you rotated your map (“map1”) to go with some other map (“map2”), you could create a new map (“map3”) by resampling map1 on the grid of map2 with the “vop resample” command.

Please see “Saving Maps After Fitting” here for the details and links:

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 2, 2015, at 1:49 PM, Li, Zongli <Zongli_Li at hms.harvard.edu> wrote:

> Hi Elain,
> Happy new year!
> I would like to rotate a single mrc density map to a specific orientation and then save it with the new orientation,
> how can I do it in Chimera?
> Thanks!
> Zongli

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