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@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