[chimerax-users] how to vizualise hydrogen bonds between ligand and back-bone of protein?
Enrico Martinez
jmsstarlight at gmail.com
Mon Mar 21 02:28:18 PDT 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 <meng at cgl.ucsf.edu>:
>
> 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 <chimerax-users at cgl.ucsf.edu> 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 <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
> >>>>
> >>
> >
> >
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>
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