[chimerax-users] how to vizualise hydrogen bonds between ligand and back-bone of protein?

Tue Mar 15 09:20:52 PDT 2022

Those "slop" values are tolerances, not the scope (cutoff):  i.e. they are added to increase the allowed ranges of values for the specific types of atoms.  A distSlop of 0.8 does not mean distance cutoff 0.8, it means 0.8 + the strict cutoff (which might be 3.0 or something like that, for a total of 3.8).

Reasons to not find the H-bond:  

- maybe your atom specification is wrong... in fact I have no idea what the "}" are in your command, they look wrong.  However, that would probably cause an error message and you would not get any H-bonds at all.  Since you are getting some H-bonds maybe that is not the problem.

- maybe those types of atoms are not considered by the H-bond detection.  I.e. it does not consider C to be an H-bonding type of atom.

- maybe it is because the H-bond geometry is very poor, you still need to increase the slop values even more to find it.

However: We believe that Chimera and ChimeraX provide high-quality H-bond detection with the default parameters (or with small increases in the distSlop and angleSlop), so it is unclear why you think your other program finding the H-bond is more correct.  Maybe it should not be considered an H-bond.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 15, 2022, at 8:17 AM, Enrico Martinez <jmsstarlight at gmail.com> wrote:
> 
> Hello again!
> I've just make a test for several docking poses and I confirm that the
> hydrogen bond between ligand and backbone atoms never could be
> detected by chimera using
> hbonds #1.1-14}&protein restrict #1.1-14}&ligand coordsets false
> interModel false makePseudobonds false log true intraRes false
> saveFile log.txt
> 
> I tried to increase significantly the distance scope to 0.8 and the
> angle scope to 40 but the interactions could not be detected. Could it
> be the problem with the command that I am using ?
> Many thanks in advance!
> 
> пн, 14 мар. 2022 г. в 15:38, Enrico Martinez <jmsstarlight at gmail.com>:
>> 
>> Thank you very much, Elaine!
>> Indeed, I found that these two options influence the results.
>> Cheers,
>> Enrico
>> 
>> чт, 10 мар. 2022 г. в 19:46, Elaine Meng <meng at cgl.ucsf.edu>:
>>> 
>>> Hello,
>>> Specifications like "#1.1&protein" already include the backbone atoms -- they are part of the protein.
>>> 
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin>
>>> 
>>> Maybe the H-bond(s) that you think should be found are less favorable (longer distance and/or poorer angle).  In that case you could try using larger values than the defaults with the "distSlop" and/or "angleSlop" options of "hbonds" to make detection more permissive.
>>> 
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html#options>
>>> 
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>>> On Mar 10, 2022, at 3:28 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>>> 
>>>> Dear ChimeraX users!
>>>> I am using the following command to calculate and save in the log
>>>> information regarding hydrogen bonds based on the consideration of
>>>> multi-frame pdb of the complex
>>>> 
>>>> # calculate hydrogen bonds for the first 14 frames of pdb
>>>> hbonds #1.1-14}&protein restrict #1.1-14}&ligand coordsets false
>>>> interModel false makePseudobonds false log true intraRes false
>>>> saveFile log.txt
>>>> 
>>>> which gives me something like this:
>>>> structure_name:
>>>> 18 H-bonds
>>>> H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
>>>> #1.1/? ASN 142 ND2    #1.1/A UNL 1 N        #1.1/? ASN 142 2HD2   3.313  2.522
>>>> #1.1/? SER 144 N      #1.1/A UNL 1 O        #1.1/? SER 144 H      2.953  2.224
>>>> #1.1/A UNL 1 O        #1.1/? LEU 141 O      #1.1/A UNL 1 H        2.753  1.877
>>>> #1.2/? ASN 142 ND2    #1.2/A UNL 1 N        #1.2/? ASN 142 2HD2   3.240  2.429
>>>> #1.2/A UNL 1 O        #1.2/? HIS 163 NE2    #1.2/A UNL 1 H        3.317  2.389
>>>> #1.3/? SER 144 N      #1.3/A UNL 1 O        #1.3/? SER 144 H      3.005  2.272
>>>> #1.3/A UNL 1 O        #1.3/? LEU 141 O      #1.3/A UNL 1 H        2.738  2.098
>>>> #1.3/A UNL 1 O        #1.3/? SER 144 OG     #1.3/A UNL 1 H        3.054  2.250
>>>> #1.6/A UNL 1 O        #1.6/? HIS 163 NE2    #1.6/A UNL 1 H        3.172  2.528
>>>> #1.7/? CYS 145 SG     #1.7/A UNL 1 O        #1.7/? CYS 145 HG     3.828  2.949
>>>> #1.7/A UNL 1 O        #1.7/? LEU 141 O      #1.7/A UNL 1 H        3.201  2.393
>>>> #1.8/? GLY 143 N      #1.8/A UNL 1 O        #1.8/? GLY 143 H      3.060  2.238
>>>> #1.8/? HIS 163 NE2    #1.8/A UNL 1 O       no hydrogen            3.084  N/A
>>>> #1.9/? GLN 189 NE2    #1.9/A UNL 1 O        #1.9/? GLN 189 1HE2   3.148  2.139
>>>> #1.10/? GLN 189 NE2   #1.10/A UNL 1 O       #1.10/? GLN 189 1HE2  2.941  2.289
>>>> #1.10/A UNL 1 O       #1.10/? GLN 189 OE1   #1.10/A UNL 1 H       2.985  2.213
>>>> #1.11/? GLN 189 NE2   #1.11/A UNL 1 O       #1.11/? GLN 189 1HE2  2.803  1.910
>>>> #1.14/? ASN 142 ND2   #1.14/A UNL 1 O       #1.14/? ASN 142 2HD2  3.199  2.369
>>>> -----------------------------------------------------------------------------
>>>> 
>>>> I noticed that in the log there is always information regarding
>>>> interactions between the ligand and the side chains of the protein but
>>>> nothing regarding hydrogen bonds involved backbone of the protein
>>>> (Which is confirmed by X-ray data for my complex). for the test I used
>>>> py at ol to visualise h-bonds and may see in the 12th frame the hydrogen
>>>> bond involved backbone of the protein.. How could I modify my script
>>>> to consider additional hydrogen bonds involving backbone atoms ?
>>>> Thank you very much in advance!
>>>> Cheers
>>>> Enrico
>>> 
> 