[Chimera-users] XPLOR volumetric data not shown as a volume

[Elaine Meng]

Dear Matthias,
Not to worry, I believe all is well -- by default, if the data is over a certain size, only part is shown at first.  It is not related to the format.  You can just show the whole thing, and you can adjust the initial display options to your liking.

Show the whole thing:  In the "Plane" section of the Volume Viewer dialog (if that is not shown, choose "Planes" from its Features menu), click the "All" button.  You may also want to change the display Style from solid (which is automatically used for planes) to surface or mesh.

Change the initial display setting:  show display settings in the Volume Viewer dialog by choosing "Data display options" from its Features menu.  See the options "Show data when opened..." and "Show plane when data larger than..."  If you want your changes to apply to future uses of Chimera, choose "Save default dialog settings" from the Features menu.

<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

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

On Aug 18, 2011, at 3:31 AM, <matthias.gutmann at stfc.ac.uk> wrote:

> Dear all,
>                 having succeeded in writing an XPLOR data file and importing it into CHIMERA, I was expecting to see
> a cube like volume. Instead, I’m only seeing a thin plane. Is this to be expected?
>  
> The header for the XPLOR file is as below:
>  
>  
>        1
> SXD2001reciprocal_space_volume
>      301       0     300     301       0     300     301       0     300
>     30.10000    30.10000    30.10000    90.00000    90.00000    90.00000
> ZYX
>        0
>      0.57280     0.05125     0.25826     0.23192     0.47232     0.40565
>      0.28667     0.06406     0.13678     0.22750     0.22332     0.11380
>     -0.02432     0.32358     0.22395     0.06303     0.22736     0.27504
>      0.30512     0.21062     0.26810     0.15033     0.25180     0.39434
>      0.85280     0.25197     0.07160     0.22430     0.28253     0.11386
>      0.34160     0.32177    -0.03150     0.22739     0.47072    -0.00241
>      0.26013     0.20844     0.20823     0.30089     0.40608     0.23863
>    -0.13479     0.28377     0.08277     0.25996     0.23550     0.09638
>  
> How can I get the entire volume to display as a volume rather than a single plane?
>  
> Is the XPLOR format not a good one to use for this purpose?
>  
> Many thanks and best wishes, 
> Matthias