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@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@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