Hi,

Following my previous post, I now have the volumes rotated and shifted as wanted.

I was wondering if I could merge them all together as 1 volume.

I did a quick search and found that it should be possible using the chimera map format.

So I saved my volumes as cmap format ( eg. volume #95 save 95.cmap) and now I tried to save them all into one file. 'volume all save volume.cmap' but I get the same 'mrc error' as when I tried with the original mrc volumes ('valueErro: Cannot write multiple volumes using format mrc')

Am I missing something?

On Fri, Apr 27, 2012 at 12:49 PM, Tom Goddard <goddard@sonic.net> wrote:

Hi Ludovic,

 As Elaine says the map file formats don't support rotated grids so you'd have to resample the map with "vop resample".   You could specify the grid using a copy of the map in the unrotated position and use the "boundingGrid true" option so that the bounds of the new resampled map are chosen to cover the entire rotated and shifted map.  For example, "vop resample #1 onGrid #0 boundingGrid true".

 As for doing the rotation, no Chimera command accepts Euler angles.  But a Python script can do it.  I've attached an example.  To rotate volume #0 using Euler angles 45,60,20 (using z-x-z "chi-convention") and then translate by 15, 33.5, -10 Angstroms start Chimera in the directory containing the attached eulermove.py script, open the volume and use:

   runscript eulermove.py #0 45 60 20 15 33.5 -10

The result will be two new volumes, one being a copy of the original volume rotated and translated, and the other being a resampled version of the rotated translated map on the original grid.  The original map stays in the same place.

 Tom

On Apr 27, 2012, at 9:26 AM, Ludovic Renault wrote:

Hi Elaine,
I have 120 or so 3d volumes (EM maps). They are all equivalent and are centered at the same position.
I would like to move each one of these 120 volumes by a specific value in terms of euler angles and shift (in pixels I assume). I can use the 'trAnsform coordinates' tool but then if I save the map, it is not saved with the new coordinates.
So
1- How to (Or can I) save the new coordinates for each volume?
2- Can I use command lines to automate the process for example by giving the command a text file with the specific coordinates for each volume?

I did do the rotation with spider software, but the shifting doesn't work because the volume(s) go outside of the box. So if all the above is not doable, is it possible to increase the volumes boxe size in chimera, then I could use the shift function in spider?

I hope I'm clear enough.
Thanks,
Ludovic

Hi Ludovic,
It is recommended to send Chimera questions to the chimera-users list (CC'd) -- I'm not the top expert on volumes, so others may have better answers!

I think the shift in Transform Coordinates is not in pixels but in units of length.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html>

How the volume grid units map to units of length can be viewed by using Features...Coordinates in the Volume Viewer menu.

Chimera has commands for translation (move) and rotation (turn) in X,Y,Z coordinate systems, but I don't know of a command to apply Euler rotations.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>

About saving a transformed map:
The map formats don't include transformation information, so there is no way to save EXACTLY the same data, except transformed. However, you can resample the map onto a new grid, and then save the new map.  The values at the new grid points are determined by interpolation, so there will be some (generally minor) data loss.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>

The resampling of one map onto the grid of another can be done with command "vop resample", for example:

vop #1 resample onGrid #0

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>

To save the new resampled volume to a file, you could use "File... Save Map as" in the Volume Viewer dialog or the command "volume" with its  "save" option.

However, I see that "vop resample" is most pertinent for saving a map that has been fitted to another.  In your case you are simply transforming the map, so it is unclear on what grid you could resample. Maybe there is some way to make a "dummy" grid in the right place.

Although "vop cover" extends a map, it assumes periodicity of that map, whereas I assume you want zeroes in the expanded parts.  Perhaps expanding a map with zeroes could be done using "vop add" to add a dummy zero map to your data set of interest.

Sorry I couldn't give a more complete solution,
Elaine

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