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.

Tom

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 mailto: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