[Chimera-users] transform coordinates of multiple volumes

Tom Goddard goddard at sonic.net
Thu May 3 10:29:40 PDT 2012

Hi Ludovic,

   Yes you need to specify the file format in the volume save command.  
Otherwise it always uses MRC -- it is not smart enough to look at the 
file suffix and choose the right format.

     volume all save v.cmap saveFormat cmap

I'll add a request to make the volume command look at the file suffix to 
determine the desired format when none is specified.


> 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 at sonic.net 
> <mailto:goddard at 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

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