XPLOR volumetric data not shown as a volume
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 ---------------------------------------------------------------------------------------------- Matthias Gutmann Instrument Scientist SXD Rutherford Appleton Laboratory Phone: +44 (0)1235 44 6397 ISIS Facility Fax: +44 (0)1235 44 5200 Chilton Didcot Office : R3, 1.28 Oxfordshire OX11 0QX Email: Matthias.Gutmann@stfc.ac.uk UNITED KINGDOM -- Scanned by iCritical.
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/fram...> 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@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
Hi Matthias, Regarding your question of whether XPLOR format is best for you. The main drawbacks are that the files are large and slow to read because they are text instead of binary. Your files are probably 2 to 3 times larger (about 8 to 12 bytes per value versus 4 bytes in binary format) and maybe 10x slower to parse since the text numbers have to be converted to binary. Most map formats are binary for these reasons. But those formats can be harder to write out since the headers are often not well documented, or are complex. So stick with XPLOR if the size and speed are ok. Tom
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
----------------------------------------------------------------------------------------------
Matthias Gutmann Instrument Scientist SXD
Rutherford Appleton Laboratory Phone: +44 (0)1235 44 6397
ISIS Facility Fax: +44 (0)1235 44 5200
Chilton Didcot Office : R3, 1.28
Oxfordshire OX11 0QX Email: Matthias.Gutmann@stfc.ac.uk
UNITED KINGDOM
-- Scanned by iCritical.
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participants (3)
-
Elaine Meng -
matthias.gutmann＠stfc.ac.uk -
Tom Goddard