[Chimera-users] command line "vol all style surface plane z, 60, 8

Dieter Blaas dieter.blaas at meduniwien.ac.at
Fri Jan 8 23:56:57 PST 2021

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 at 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 at 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 at 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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