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

[Elaine Meng]

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