opened
hainm
username_0
hi,

Please see the figure (I used recent `ngl` version in `nglview`).

![ace_nme](https://cloud.githubusercontent.com/assets/4451957/19702679/bc049666-9ace-11e6-8e81-e7d9d919142b.png)

pdb 

```bash
ATOM      1 HH31 ACE     1       2.000   1.000  -0.000  1.00  0.00           H  
ATOM      2  CH3 ACE     1       2.000   2.090   0.000  1.00  0.00           C  
ATOM      3 HH32 ACE     1       1.486   2.454   0.890  1.00  0.00           H  
ATOM      4 HH33 ACE     1       1.486   2.454  -0.890  1.00  0.00           H  
ATOM      5  C   ACE     1       3.427   2.641  -0.000  1.00  0.00           C  
ATOM      6  O   ACE     1       4.391   1.877  -0.000  1.00  0.00           O  
ATOM      7  N   ALA     2       3.555   3.970  -0.000  1.00  0.00           N  
ATOM      8  H   ALA     2       2.733   4.556  -0.000  1.00  0.00           H  
ATOM      9  CA  ALA     2       4.853   4.614  -0.000  1.00  0.00           C  
ATOM     10  HA  ALA     2       5.408   4.316   0.890  1.00  0.00           H  
ATOM     11  CB  ALA     2       5.661   4.221  -1.232  1.00  0.00           C  
ATOM     12  HB1 ALA     2       5.123   4.521  -2.131  1.00  0.00           H  
ATOM     13  HB2 ALA     2       6.630   4.719  -1.206  1.00  0.00           H  
ATOM     14  HB3 ALA     2       5.809   3.141  -1.241  1.00  0.00           H  
ATOM     15  C   ALA     2       4.713   6.129   0.000  1.00  0.00           C  
ATOM     16  O   ALA     2       3.601   6.653   0.000  1.00  0.00           O  
ATOM     17  N   ALA     3       5.846   6.835   0.000  1.00  0.00           N  
ATOM     18  H   ALA     3       6.737   6.359  -0.000  1.00  0.00           H  
ATOM     19  CA  ALA     3       5.846   8.284   0.000  1.00  0.00           C  
ATOM     20  HA  ALA     3       5.332   8.648  -0.890  1.00  0.00           H  
ATOM     21  CB  ALA     3       5.135   8.833   1.232  1.00  0.00           C  
ATOM     22  HB1 ALA     3       5.643   8.485   2.131  1.00  0.00           H  
ATOM     23  HB2 ALA     3       5.150   9.922   1.206  1.00  0.00           H  
ATOM     24  HB3 ALA     3       4.102   8.485   1.241  1.00  0.00           H  
ATOM     25  C   ALA     3       7.266   8.832   0.000  1.00  0.00           C  
ATOM     26  O   ALA     3       8.229   8.068  -0.000  1.00  0.00           O  
ATOM     27  N   ALA     4       7.394  10.161   0.000  1.00  0.00           N  
ATOM     28  H   ALA     4       6.572  10.747   0.000  1.00  0.00           H  
ATOM     29  CA  ALA     4       8.692  10.805  -0.000  1.00  0.00           C  
ATOM     30  HA  ALA     4       9.246  10.507   0.890  1.00  0.00           H  
ATOM     31  CB  ALA     4       9.500  10.412  -1.232  1.00  0.00           C  
ATOM     32  HB1 ALA     4       8.962  10.712  -2.131  1.00  0.00           H  
ATOM     33  HB2 ALA     4      10.469  10.910  -1.206  1.00  0.00           H  
ATOM     34  HB3 ALA     4       9.647   9.332  -1.241  1.00  0.00           H  
ATOM     35  C   ALA     4       8.551  12.320   0.000  1.00  0.00           C  
ATOM     36  O   ALA     4       7.439  12.844   0.000  1.00  0.00           O  
ATOM     37  N   NME     5       9.685  13.026   0.000  1.00  0.00           N  
ATOM     38  H   NME     5      10.576  12.550   0.000  1.00  0.00           H  
ATOM     39  CH3 NME     5       9.685  14.475   0.000  1.00  0.00           C  
ATOM     40 HH31 NME     5       8.657  14.839   0.000  1.00  0.00           H  
ATOM     41 HH32 NME     5      10.198  14.839   0.890  1.00  0.00           H  
ATOM     42 HH33 NME     5      10.198  14.839  -0.890  1.00  0.00           H  
END   
```
ACE and NME amber resnames
issue
created
arose
username_1
It would indeed be nice to have automatic bounds for common peptide capping groups

- ACE (N-terminal)
- NME (C-terminal)
comment
created
arose
username_1
are there more common peptide capping groups you know @username_0 (or anyone else)?
comment
created
hainm
username_0
1.

![image](https://user-images.githubusercontent.com/4451957/30569987-352848be-9cac-11e7-8f1b-3e631a2624bf.png)

2. Amine ending group	   NHE
comment
created
arose
username_1
Do you have example files for those?
comment
created
arose
username_1
would need residue and atom names
comment
created
hainm
username_0
Will update later.
comment
created
hainm
username_0
- NME
```
HETATM    1  N   NME     1       3.326   1.548  -0.000  0.00  0.00           N  
HETATM    2  H   NME     1       3.909   0.724  -0.000  0.00  0.00           H  
HETATM    3  CH3 NME     1       3.970   2.846  -0.000  0.00  0.00           C  
END                                                                             
```

- NHE
```
HETATM    1  N   NHE     1       2.194   1.598  -0.000  0.00  0.00           N  
HETATM    2  HN1 NHE     1       3.035   1.039  -0.000  0.00  0.00           H  
HETATM    3  HN2 NHE     1       2.250   2.606  -0.000  0.00  0.00           H  
END                                                                             
```

- ACE
https://github.com/username_1/ngl/issues/224#issue-185223637
comment
created
tmgriffiths
username_2
There's a couple extra termini I can think of for building proteins for molecular dynamics.

- C-termini form the Charm36 FF
   - O-methyl (C(=O)OCH3)
   - amide (C(=O)NH2)

There's a couple specific to proline too. I'll put these and atoms names for all up later.
comment
created
arose
username_1
Gave this some thought and I think this is better solved by general distance-based bond perception.
comment
created
hainm
username_0
A good plan.
comment
created
arose
username_1
added a quick fix to look for bonds from non-polymers to other groups, see 8a0a81d1f8d0e1f6620ca23be8fdb37fd1f9a50a
comment
created
arose
username_1
Does the trick for @username_0's example

![screenshot 64](https://user-images.githubusercontent.com/272250/31142493-500fbaf2-a82f-11e7-8d09-338e8f428ce0.png)
comment
closed
arose
username_1
issue
created
hainm
username_0
Kool
comment
created
hainm
username_0
@username_1 is this change in beta 3 yet?

I still see the unbond here.

<img width="818" alt="screen shot 2017-10-05 at 7 56 25 pm" src="https://user-images.githubusercontent.com/4451957/31257585-53d6e726-aa07-11e7-9665-27b8fd9dcc8d.png">

line repr is fine.

<img width="1145" alt="screen shot 2017-10-05 at 7 57 15 pm" src="https://user-images.githubusercontent.com/4451957/31257602-708b2e68-aa07-11e7-8edb-414f32b59432.png">

may be different issue?
comment
created
arose
username_1
yeah, different issue, basically need and option to display bonds when only one of the atoms is in the selection
comment