[chimerax-users] Question about pad parameter

[Elaine Meng]

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