[chimerax-users] Question about pad parameter

[Thu Nguyen]

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


On Fri, Nov 4, 2022 at 6:29 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello,
> The pad values are in whatever physical units of distance your data are
> in, usually angstroms (and certainly your PDB structure is in angstroms).
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover>
>
>  I wouldn't know offhand how big the "voxels" are in your map, but you can
> see a list of many settings for the map including voxel size with command
> "volume settings" and then convert from that angstrom voxel size to the pad
> value that you want.
>
> 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 4, 2022, at 9:32 AM, Thu Nguyen via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hello,
> > I am using the volume cover command to crop the chain from the protein
> map. Here is what I did:
> > > open 12554 from emdb
> > > open 7ns0
> > > volume cover #1 atomBox #2/A1 pad 1.0
> > Suppose I want to add extra 17 voxels on each size of the chain, what
> value of pad should I add? Also, could you tell me the unit of pad in this
> command?
> > Thank you very much.
> >
> > Best regards,
> > Thu
>
>
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