[Chimera-users] Orienting mol maps in space?

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 16 14:50:50 PDT 2021

Hi Cynthia,
I believe you would need to open both maps (let's call them "pink" and "yellow" according to your image) and then turn the pink one 90 degrees *without moving the yellow one* before resampling the pink one on the grid of the yellow one.  E.g. if the pink one is #1, command

turn y 90 mod #1

... and then do the resampling.

Saving rotated maps is discussed at the bottom of this page:

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

> On Mar 16, 2021, at 2:26 PM, Cynthia Lee Page <cynthia.page at colorado.edu> wrote:
> HI,
> I am a newbie with Chimera. I have learned a lot in this process of making reference maps for use in Relion, thanks to the tutorials and rich information available on this list and in the documentation for Chimera. 
> I have followed this tutorial cool tutorial (https://www.cgl.ucsf.edu/chimera/videodoc/MicrotubuleSym/index.html) for making 14 pf tubes (using EMDB 5194), 1JFF ( alpha/beta tubulin) plus the A chain of 3B6U (KIF3B) to represent the monomer of this motor protein.
> I made a 15 resolution mol map of the resulting model, then cropped off the ends to make the volume flush at the MT ends using the Subregion selection feature in the Volume Viewer. 
> When I open this map in Chimera it does not open as other mrc files open. Specifically, instead of looking down the microtubule (considered Z axis, I believe) I am looking at the X-Y axis. “Centering" the map in Volume Viewer only centers it horizontally, “orienting” the file does nothing. Where as, if I orient any other reference files (including Relion generated 3D.mrc files) the map volume will orient so that the viewer is looking down the microtubule. Please see the attache image, the yellow volume centers/orients correctly, the pink volume is the one I made via the tutorial and doesn’t orient.
> I am guessing I am missing a coordinate system to align this volume in space but I haven’t been able to figure out how to add this information to my mrc file. I am also assuming that this orientation information is important to include in the mrc file formats. 
> Any help or insight much appreciated!
> Thanks,
> Cynthia
> PS I did try to "vop resample onGrid” using pink onto the yellow models and learned that’s how you can create the same voxel size (!), but it did not change the orientation capabilities of the pink model.
> <Screen Shot 2021-03-16 at 2.51.31 PM.png>

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