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

21 Mar 2022


      Hello Elaine
Many thanks for these kind suggestions!
In fact this back-bone H-bond has been validated by X-ray data
(observed in several structures of my protein) and then by my docking
studies. Please find enclosed the picture of this interaction: as we
may see it is located on the relatively short distance between the O
atom of the ligand and the HN of the backbone of the Glu residue. I
believe it has to match both default slope criteria....

Regarding my command, actually I used it with batch version of
chimeraX (in the script) so the goal was not to display the
interactions but rather to save it directly into the log file:

# calculate h-bonds between first 10 models from multi-model pdb file
hbonds #1.1-10&protein restrict #1.1-10&ligand coordsets false
interModel false makePseudobonds false log true intraRes false
saveFile log_hbondsALL.log

It produces a log with the correct H-bonds with the exemption of the
interaction shown on the screenshot (which is always detected by other
programs...)
With best regards,
Enrico

вт, 15 мар. 2022 г. в 17:28, Elaine Meng :
...
I see you are not displaying the H-bonds in your command anyway, but another thing that confuses some people is that even though the H-bond is found (i.e. it is counted and listed in the Log) it is not displayed because the atoms are not displayed.
In other words, if you are using the display to judge whether the H-bond is found you would need to use the "hbond" command options:
makePseudobond true reveal true
https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html#options
Elaine
...
On Mar 15, 2022, at 9:20 AM, Elaine Meng via ChimeraX-users  wrote:
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  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 :
...
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 :
...
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  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@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
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