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

Tue Mar 15 08:17:40 PDT 2022

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
> >