[chimerax-users] Question about pad parameter

[Thu Nguyen]

Hi Mr. Tom,
Thank you very much for your help. It is exactly what I was looking for.
The ChimeraX Recipes are extremely helpful, too.

Best regards,
Thu

On Mon, Nov 7, 2022 at 9:07 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Thu,
>
>   It sounds like you are trying to automate some processing.  If you want
> to write out the region bounds with Python you could put this code in
> bounds.py and open it in ChimeraX after opening your map data.
>
> from chimerax.map import Volume
> with open('bounds.txt', 'w') as output:
>   for v in session.models:
>     if isinstance(v, Volume):
>       (i0,j0,k0), (i1,j1,k1) =  v.region[:2]
>       output.write(f'{v.name.replace(" ","_")} {i0} {j0} {k0} {i1} {j1}
> {k1}\n')
>
> There are many examples of ChimeraX Python scripts at the ChimeraX Recipes
> web site
>
> https://rbvi.github.io/chimerax-recipes/
>
>   Tom
>
> On Nov 7, 2022, at 8:40 AM, Thu Nguyen via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Good morning,
> Thank you very much for your explanation. It is truly helpful.
> For my second question, is there a way to write the region of a map to a
> text file? For example, when I open the map of emdb 12554, I have the
> region of 0 0 0 to 449 449 449. Is there any way we can write these numbers
> into a text file (for example: id_12554 0 0 0 449 449 449)?
> Thank you very much.
>
> Best regards,
> Thu
>
>
> On Mon, Nov 7, 2022 at 11:26 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>> Hi Thu,
>> The pad value units are angstroms (not voxels) but it sounds like you
>> understand that, since your math is correct: if you want 1.4 angstroms,
>> then enter 1.4.  If you want 23.8 angstroms then enter 23.8.  If the voxel
>> size (grid spacing) is 1.4 then those are equal to 1 grid unit and 17 grid
>> units respectively, like you said.
>>
>> To calculate the XYZ location of grid indices, like (0,0,0) and
>> (103,95,143) you have to figure it out from the voxel size and origin
>> coordinates, as reported by "volume settings" command.  Say for example
>> that this command gives me
>>
>> voxel size = 1.4 1.4 1.4
>> origin = 2.525 -2.214 7.929
>>
>> Then the coordinates of grid (0,0,0) are xyz (2.525,-2.214,7.929).  The
>> coordinates of grid (1,3,1) are x = 2.525 + 1(1.4) = 3.925, y = -2.214 +
>> 3(1.4) = 1.986, z = 7.929 + 1(1.4) = 9.329.
>>
>> For saving part of a map, you can enter grid indices with the "save"
>> command "region" option, for example if your map is #2:
>>
>> save ~meng/Desktop/mymap.mrc model #2 region 0,0,0,103,95,143
>>
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>
>> > On Nov 7, 2022, at 7:44 AM, Thu Nguyen via ChimeraX-users <
>> chimerax-users at cgl.ucsf.edu> wrote:
>> >
>> > Thank you very much for your help.
>> >
>> > You mean that if the voxel size of my map is 1.4 (for example), then
>> the pad value in the command will have the unit of the voxel size, which is
>> 1.4 in this case? And if I want to add 17 extra voxels on each side, the
>> pad value will be 1.4*17 = 23.8?
>> >
>> > I do have another question about how to extract a region of a chain.
>> For example, if a chain has its region of 0 0 0 to 103 95 143, how do we
>> extract its location and save it in a text file?
>> > Thank you so much.
>> >
>> > Best regards,
>> > Thu
>>
>> <Screen Shot 2022-11-07 at 11.33.31 AM.png>
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