nevermind, I was entering @distance.py instead of run distance.py
On Fri, Oct 13, 2017 at 2:05 PM, Leigh M <leigh.j.man...@gmail.com> wrote:
> Hi Jared-
>
> I just use the C-alpha xyz coordinates and use d = math.sqrt(dx**2 +
> dy**2 + dz**2).
> I've been using python alone without pymol...using your code with the
> pymol api works for individual distances but I'm calculating hundreds of
> distances and need to write to a csv which does not seem to be working.
> I get an error: NameError: name 'csvfile' is not defined
>
> for k,v in AA_dict.items():
> vA = v[0:3]
> for k2, v2 in AA_dict.items():
> vA2 = v2[0:3]
> point1 = '/5p21//A/'+ vA2 + '`' + str(k2) + '/CA'
> point2 = '/5p21//A/' + vA + '`' + str(k) + '/CA'
> o = cmd.get_coords(point1)[0]
> h = cmd.get_coords(point2)[0]
> dx = h[0] - o[0]
> dy = h[1] - o[1]
> dz = h[2] - o[2]
> d = math.sqrt(dx ** 2 + dy ** 2 + dz ** 2)
> dist_dict[(v, v2)] = d
>
> with open(protein + '_distances.csv', 'w') as csvfile:
> fieldnames = dist_dict.keys()
> writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
> writer.writeheader()
> writer.writerow(dist_dict) # writes the chi angles
> csvfile.close()
>
>
> Thanks
>
> Leigh
>
> On Thu, Oct 12, 2017 at 8:44 PM, Jared Sampson <jared.samp...@columbia.edu
> > wrote:
>
>> 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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