Hi Leigh -
How are you getting the coordinates? This works for me:
```
import math
# Show more digits for the distance label
set label_distance_digits, 10
# Make an alanine residue
fab A, ala
# Get coordinates from 2 atoms
o = cmd.get_coords("/ala///1/O")[0]
h = cmd.get_coords("/ala///1/H")[0]
# Calculate the distance
dx = h[0] - o[0]
dy = h[1] - o[1]
dz = h[2] - o[2]
d = math.sqrt(dx**2 + dy**2 + dz**2)
print(d)
# Distance from script: 2.3546268062493567
# Distance from wizard: 2.354626655 (label maxes out at 10 digits)
```
Those values seem close enough to me. Is it possible that in your script
you're getting the coordinates for the i+1 or i-1 atom instead, or a different
state? Or maybe picking the other side of a symmetric side chain (e.g. OD1 vs
OD2)? If you could share the relevant portion of the script, you might get
some more useful feedback; right now all we can do is guess!
Cheers,
Jared
On October 12, 2017 at 2:19:36 PM, Leigh M (leigh.j.man...@gmail.com) wrote:
Anyone know how pymol calculates distance between two atoms?
I wrote a python script that calculates distance using the distance formula and
the xyz coordinates in the pdb, and it differs from the wizard by ~40%. Any
ideas on what might be going on would be helpdul
Thanks!
Leigh
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