[chimerax-users] Question about pad parameter

[Thu Nguyen]

Thank you so much for your help.
Have a great day.

Best regards,
Thu

On Mon, Nov 7, 2022 at 11:45 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> As far as I know you would need to use "volume settings" to show the info
> in the Log and then just copy/paste yourself into some other text editor to
> create a text file.  Or save the whole Log (e.g. command "log save") but
> that will give an HTML file, not a text file.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save>
>
> Elaine
>
>
>
> > 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
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>
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