command line "vol all style surface plane z,60,8
Hi, I am trying to display a volume (128 px box) sliced through the middle as seen down the z axis but 8 slices thick instead of just one. I can render a single slice with "vol #0 style surface plane z,64" but I could not find out how to make it e.g. 8 slices thick. In VolumeViewer there is the parameter 'Depth' but it is not accepted as parameter in the command line! Rater, adding one more number at the end of the command starts playing a movie of one slice after the other.... Thanks a lot for hints, bw Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
Hi Dieter, The volume command documentation gives syntax for the "planes" option: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes> As explained in the above, it would be something like volume #0 style surface planes z,64,64,1,8 ...where the last number in the comma-separated list is the depth. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 7, 2021, at 11:06 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi, I am trying to display a volume (128 px box) sliced through the middle as seen down the z axis but 8 slices thick instead of just one.
I can render a single slice with "vol #0 style surface plane z,64" but I could not find out how to make it e.g. 8 slices thick. In VolumeViewer there is the parameter 'Depth' but it is not accepted as parameter in the command line! Rater, adding one more number at the end of the command starts playing a movie of one slice after the other....
Thanks a lot for hints, bw Dieter
Hi Dieter, Sometimes I find it easier to use the volume command to specify the exact region bounds with the "region" option volume #0 region 0,0,60,127,127,67 The six numbers are the i,j,k minimum grid index and i,j,k maximum grid index. Indices start at 0. Tom
On Jan 8, 2021, at 8:37 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dieter, The volume command documentation gives syntax for the "planes" option: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes>
As explained in the above, it would be something like
volume #0 style surface planes z,64,64,1,8
...where the last number in the comma-separated list is the depth. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 7, 2021, at 11:06 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi, I am trying to display a volume (128 px box) sliced through the middle as seen down the z axis but 8 slices thick instead of just one.
I can render a single slice with "vol #0 style surface plane z,64" but I could not find out how to make it e.g. 8 slices thick. In VolumeViewer there is the parameter 'Depth' but it is not accepted as parameter in the command line! Rater, adding one more number at the end of the command starts playing a movie of one slice after the other....
Thanks a lot for hints, bw Dieter
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Dear Tom, dear Elaine, thank you very much for your hints! They are most useful! So far I prefer Elaine's version as it requires the change of only one parameter to flipp back to seeing the entire volume like so: volume #0 style surface planes z,64,64,1,*8* >>> volume #0 style surface planes z,64,64,1,*128* whereas Tom's requires two: volume #0 region 0,0,*60*,127,127,*67* >>> volume #0 region 0,0,*1*,127,127,*128 * best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ On 09.01.2021 00:34, Tom Goddard wrote:
Hi Dieter,
Sometimes I find it easier to use the volume command to specify the exact region bounds with the "region" option
volume #0 region 0,0,60,127,127,67
The six numbers are the i,j,k minimum grid index and i,j,k maximum grid index. Indices start at 0.
Tom
On Jan 8, 2021, at 8:37 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dieter, The volume command documentation gives syntax for the "planes" option: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes>
As explained in the above, it would be something like
volume #0 style surface planes z,64,64,1,8
...where the last number in the comma-separated list is the depth. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 7, 2021, at 11:06 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi, I am trying to display a volume (128 px box) sliced through the middle as seen down the z axis but 8 slices thick instead of just one.
I can render a single slice with "vol #0 style surface plane z,64" but I could not find out how to make it e.g. 8 slices thick. In VolumeViewer there is the parameter 'Depth' but it is not accepted as parameter in the command line! Rater, adding one more number at the end of the command starts playing a movie of one slice after the other....
Thanks a lot for hints, bw Dieter
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participants (3)
-
Dieter Blaas -
Elaine Meng -
Tom Goddard