[Chimera-users] transform coordinates of multiple volumes
goddard at sonic.net
Thu May 3 10:29:40 PDT 2012
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.
> 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
> 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.
> 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.
> 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.
> 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.
> 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.
> 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.
> The resampling of one map onto the grid of another can be done
> with command "vop resample", for example:
> vop #1 resample onGrid #0
> 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
> Sorry I couldn't give a more complete solution,
> 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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