[chimerax-users] hbonds and the number of detected interactions

[Enrico Martinez]

That's great!
Thank you very much,Elaine!
Cheers,
Enrico

вс, 30 янв. 2022 г. в 17:29, Elaine Meng <meng at cgl.ucsf.edu>:
>
> As I said before, you really should read the "hbonds" command help -- use command "help hbonds" or see the link I already sent in earlier messages.
>
> The "hbonds" command has "saveFile" and "log" options.
>
> Elaine
>
>
> > On Jan 30, 2022, at 12:33 AM, Enrico Martinez <jmsstarlight at gmail.com> wrote:
> >
> > Thanks a lot, Elaine!
> > Now I understand it completely (I hope so :-)
> > It means that the both slopes work like additional permissions over
> > the experimentally validated distances or angles. So I do not see a
> > big difference between distSlop 0.4 or 0.5, but the slope for angle
> > 40, seems to me too much.. But it depends on the specific group.
> > Well..
> > last question related to hydrogen bonds:
> > when I do it in chimeraX gui I can see very nice detailed info
> > regarding visualized h-bonds, would it be possible to save this info
> > automatically in some output.log (e.g. using save command??) , which I
> > may examine outside of the Chimera?
> > Many thanks again for your kind support
> > Have a nice and lovely Sunday
> > Enrico
> >
> > пт, 28 янв. 2022 г. в 18:36, Elaine Meng <meng at cgl.ucsf.edu>:
> >>
> >> The "slop" options are explained in the help:
> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html#options>
> >>
> >> The paper cited in the "hbonds" help page linked above has many different geometric criteria for different types of atoms.
> >>
> >> If (for example) that paper says the distance limit for a specific pair of atoms is 2.9 angstroms and the distSlop is 0.4 then it means to find ones that are up to 3.3 angstroms apart.  The orange color then means the distance was over 2.9 but within 3.3.
> >>
> >> What slop values to use is your decision.  We made the defaults to be reasonable in most situations.
> >>
> >> Elaine
> >>
> >>
> >>> On Jan 28, 2022, at 1:06 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> >>>
> >>> Thank you very much, Eric!
> >>> In fact I have already read it but there are some things not clear for me.
> >>> May you give me a small example how I could compare the slope values
> >>> of chimera with the geometric criteriums shown in the paper ? Does the
> >>> dist slope correspond to the r (A) ?
> >>> And finally how could we explain that almost all predicted h-bonds are
> >>> colored in the second (orange) colour using default slops? Assuming
> >>> that I am working with a structure of very good resolution (1.4A) does
> >>> it means that I should DECREASE the both slope values for my case?
> >>> Many thanks in advance
> >>> Enrico
> >>>
> >>> чт, 27 янв. 2022 г. в 19:52, Eric Pettersen <pett at cgl.ucsf.edu>:
> >>>>
> >>>> Hi Enrico,
> >>>>       You should really read the paper Elaine mentioned to get a feel for the range of angles and distances for various donor/acceptor types.  You also have to consider the resolution of the structure you are using and therefore the uncertainty in atomic positions (the principal reason that there are "slop" values in the calculation).  There really is no single right answer.  You have to use your judgment.
> >>>>
> >>>> --Eric
> >>>>
> >>>>> On Jan 27, 2022, at 10:15 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> >>>>>
> >>>>> Many thanks, Elaine!
> >>>>> I just wonder what may be the upper limit for the both parameters to
> >>>>> i) increase some flexibility thus allowing to consider even weaker
> >>>>> h-bonds but ii) to be realistic ;-)
> >>>>>
> >>>>> I've just recalculated again the hbond using two colors for slop, with
> >>>>> the default params 0.4 and 20
> >>>>> hbonds #1 & ligand reveal true log true radius 0.06 dashes 6 color
> >>>>> turquoise distSlop 0.4 angleSlop 20 twoColors true slopColor firebrick
> >>>>> intraRes false
> >>>>> and generally the most h-bonds were colored in firebrick meaning that
> >>>>> they could be less significant..
> >>>>> Cheers,
> >>>>> Enrico
> >>>>>
> >>>>> чт, 27 янв. 2022 г. в 18:23, Elaine Meng <meng at cgl.ucsf.edu>:
> >>>>>>
> >>>>>> It is beyond the scope of this forum to discuss the physics of  individual H-bonds or how to "validate" them. People have argued for years about different kinds of H-bonds, their relative strengths, etc.   We set default parameters to give what we think is the most reasonable results in most situations, based on a detailed published survey of H-bonding structures (see publication cited in help)... but then allow users to adjust the parameters at their own discretion.
> >>>>>>
> >>>>>> Elaine
> >>>>>>
> >>>>>>> On Jan 27, 2022, at 1:18 AM, Enrico Martinez <jmsstarlight at gmail.com> wrote:
> >>>>>>>
> >>>>>>> p.s. So based on your experience and the provided screenshot, is it
> >>>>>>> possible to validate this hydrogen bond? I believe that Glu is a very
> >>>>>>> strong negatively charged residue which normally provides
> >>>>>>> salt-bridges... BTW I analyzed another X-ray structure of the same
> >>>>>>> complex and could validate there a hydrogen bond between ligand and
> >>>>>>> the back-bone of the same Glu-166 which seems to me more bizarre (this
> >>>>>>> GLU belongs to the betta-strand part of the structure, where in the
> >>>>>>> visualization usually we may see an arrow => ) :-0
> >>>>>>>
> >>>>>>> ср, 26 янв. 2022 г. в 20:58, Enrico Martinez <jmsstarlight at gmail.com>:
> >>>>>>>>
> >>>>>>>> I gotcha!
> >>>>>>>> So eventually I could get the hbond with the Glu-166 (as i had already
> >>>>>>>> observed for the same complex using py at ol) using
> >>>>>>>> the angle slop = 40 and the distance slop= 0.6
> >>>>>>>> :-)
> >>>>>>>>
> >>>>>>>> ср, 26 янв. 2022 г. в 20:47, Elaine Meng <meng at cgl.ucsf.edu>:
> >>>>>>>>>
> >>>>>>>>> There is a misunderstanding: please read the hbonds help, the link I sent before.  The "slop" values are not the cutoffs; instead they are used to expand the ranges of the cutoffs.  There is no single angle cutoff  or distance cutoff.  Instead, many different cutoffs are used for different combinations of atom types depending on their elements and hybridization states.  These multiple cutoff values are listed in several tables in a publication cited in the help page.  If you cannot access that publication let me know.
> >>>>>>>>>
> >>>>>>>>> Also the default "slop" values are what we recommend for most PDB files.  If you increase the values very much, you may get very poor results, "bad" (or impossible) H-bonds.
> >>>>>>>>> Elaine
> >>>>>>>>>
>