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

[Enrico Martinez]

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
>