[chimerax-users] how to vizualise hydrogen bonds between ligand and back-bone of protein?
Enrico Martinez
jmsstarlight at gmail.com
Tue Mar 22 09:36:23 PDT 2022
Yep, exactly, this is what I may see with my pdb..
BTW do we have some command line solution to "reorder" the atoms in
multi-model pdb which me may do the trick "on the fly" via some
software executed in the terminal command line (without GUI)?
Cheers,
Enrico
вт, 22 мар. 2022 г. в 17:12, JAMES MICHAEL S1JJRUdFUiA= <jmkrieger at cnb.csic.es>:
>
> Hi Enrico,
>
> That sounds similar to what I did with ProDy then (except I put them
> at the beginning of each model). When I opened the resulting PDB in
> ChimeraX then the side chain atoms were disconnected and the backbone
> maybe as well. After opening in PyMOL first and saving again it was
> reordered well and they seemed to be connected up right in ChimeraX
> too. If it's still not working by doing that then you probably need to
> pass each model to some tool like MODELLER or HADDOCK individually to
> fix the incorrect bond distances etc.
>
> Best wishes
> James
>
>
> Enrico Martinez <jmsstarlight at gmail.com> escribió:
>
> > Hey James,
> > actually, it seems to me that I have already done it: copy/past a
> > receptor model (with the static residues!) into EACH of the model
> > containing docking pose of the ligand + 5 flexible residues. Here is
> > my script to produce multi-model pdb with the complex:
> >
> > awk 'NR==FNR {s = s $0 ORS; next} $0 == "ENDMDL" {$0 = s $0} 1'
> > "${temp}"/static_receptor.pdb
> > "${results}"/docking_poses_with_flexible_residues.pdb >>
> > "${results}"/complex. pdb
> >
> > basically it looks for the ENDMDL term in each frame of the
> > multi-model pdb and past there the model of the receptor. So the both
> > are present in each frames.
> >
> > The issue is related to the Flexible residues, which are always near
> > the ligand atoms (since they are present in the each model with the
> > docking poses) so the resulted "combined" PDB appeared to be
> > "fragmented" in the sence of the side-chains of the flexible residues
> > (taken from the first pdb) as well as their backbone atoms (present in
> > another pdb with the static receptor), so ..
> >
> > Although the combined PDB produced by my script seems to be absolutely
> > normal, there are problems with the recognition of the back-bone atoms
> > of the flexible residues, which are not considered as the donors for
> > the hydrogen bonds ...
> >
> > may-be there is some program which may just open my pdb and convert it
> > (the order of the string) into the normal format since the problem is
> > always related to the position of the flexible side-chains in each
> > frame...
> >
> > Enrico
> >
> > вт, 22 мар. 2022 г. в 16:12, JAMES MICHAEL S1JJRUdFUiA=
> > <jmkrieger at cnb.csic.es>:
> >>
> >> Hi Enrico,
> >> It would probably be better to combine them model by model rather than
> >> just cat-ing the two. Probably the ProDy Python API could handle this
> >> but I'm not exactly sure. You could try something along the lines of
> >> the following. I just made some PDB files that sound like what you
> >> described and it worked fine.
> >>
> >> from prody import *
> >>
> >> atoms1 = parsePDB(pdbfile1) # multi-model will be read as multiple
> >> coordinate sets
> >>
> >> atoms2 = parsePDB(pdbfile2) # I'm assuming it just has one coordinate set
> >>
> >> atoms3 = atoms2.copy()
> >>
> >> for i in range(atoms1.numCoordsets()-1):
> >> atoms3.addCoordset(atoms2)
> >>
> >> atoms4 = atoms1 + atoms3
> >>
> >> writePDB(pdbfile3, atoms4)
> >>
> >> You'd also need to open the resulting PDB file in pymol and save it
> >> again (making sure to include all states) to get the atoms back in the
> >> right order for chimerax to know they belong to the save residues.
> >>
> >> Best wishes
> >> James
> >>
> >>
> >> Enrico Martinez <jmsstarlight at gmail.com> escribió:
> >>
> >> > Hi James,
> >> > many thanks for these suggestions!
> >> > Indeed I am looking for some utility that may be useful to fix my
> >> > "fragmented" multi-model pdb, converting it into "common" format
> >> > (considering all frames).
> >> > I've just made a quick test excluding the residues where I had
> >> > difficulties with the visualisation of the "back-bone" hydrogen bond
> >> > from the list of the "flexible residues" in VINA calculations and here
> >> > it is: since this part is no more "fragmented", Chimera is able to
> >> > find the hydrogen bond with the default "slopes" values. Victory!
> >> > May be there is some command in Chimera that may fix the problem?
> >> > Essentially I am dealing with protein-ligand complex produced by the
> >> > CAT of two initial pdbs: i) multi-model pdb of the docking poses
> >> > (containing ligand and 4-5 side-chains) + the "static part" of the
> >> > protein (all of the atoms excluding these 4-5 flexible side-chains)
> >> > merged into the each model. It looks absolutely correctly while
> >> > examining it in any molecular vizualisator so the problem could only
> >> > be detected in ChimeraX..
> >> > I would be grateful for any suggestions
> >> > Cheers,
> >> > Enrico
> >> >
> >> > вт, 22 мар. 2022 г. в 12:54, JAMES MICHAEL S1JJRUdFUiA= via
> >> > ChimeraX-users <chimerax-users at cgl.ucsf.edu>:
> >> >>
> >> >> Hi Enrico,
> >> >> You may want to try rebuilding these parts with modeller or some other
> >> >> template-based modelling method. There may also be an option to refine
> >> >> the docked structure in autodock like there is in HADDOCK or an
> >> >> ability to use HADDOCK for the autodock output.
> >> >> Best wishes
> >> >> James
> >> >>
> >> >> Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
> >> escribió:
> >> >>
> >> >> > Right, thank you very much Elaine!
> >> >> > Now I gotcha! Indeed it should be the case since the pdb was produced
> >> >> > by the concatenation of the autodock results, (which left flexible
> >> >> > residues with the ligand) with the receptor pdb w/o these side-chains.
> >> >> > BTW I double checked and could reproduce the hydrogen bond with the
> >> >> > side-chain atoms of the same residue, so the problem indeed is related
> >> >> > only to backbone (particularly to the N atom)..
> >> >> > Anyway thank you very much for the help!
> >> >> > Cheers,
> >> >> > Enrico
> >> >> >
> >> >> > пн, 21 мар. 2022 г. в 19:56, Elaine Meng <meng at cgl.ucsf.edu>:
> >> >> >>
> >> >> >> The problem is that your PDB file is fragmented, i.e. you only have
> >> >> >> some of the receptor residues so the backbone chain is broken in
> >> >> >> several places. When I try to run "hbonds" on what you sent me,
> >> >> >> there is a warning message in the Log:
> >> >> >>
> >> >> >> The following atoms were skipped as donors/acceptors due to missing
> >> >> >> heavy-atom bond partners: /? MET 49 N; /? GLU 166 N; /? CYS 145 N;
> >> >> >> /? ASN 142 N; /? GLN 189 N
> >> >> >>
> >> >> >> When (for example) Glu 166 atom N does not have a bond from residue
> >> >> >> 165 atom C (because residue 165 is not in your structure), the
> >> >> >> correct angle for H-bonding is undetermined, so the hbonds
> >> >> >> algorithm ignores it. If you had the whole protein in the file, it
> >> >> >> would probably not be missing all these backbone bonds, and then it
> >> >> >> could correctly detect the H-bonds.
> >> >> >>
> >> >> >> Other programs probably have simple distance checking that doesn't
> >> >> >> use other atoms to figure out the proper angle.
> >> >> >>
> >> >> >> Whenever you get an unexpected result from a script, it is useful
> >> >> >> to try it interactively in the GUI so that you can see if there are
> >> >> >> any warning messages.
> >> >> >>
> >> >> >> I hope this clarifies the situation,
> >> >> >> Elaine
> >> >> >>
> >> >> >> > On Mar 21, 2022, at 9:09 AM, Elaine Meng via ChimeraX-users
> >> >> >> <chimerax-users at cgl.ucsf.edu> wrote:
> >> >> >> >
> >> >> >> > Hello,
> >> >> >> > We can't figure out the reason for the "missing" H-bond unless
> >> >> >> you send us the file with the ligand and receptor atomic
> >> >> >> coordinates, the same ones shown in the image.. If you didn't want
> >> >> >> to share it with the whole chimerax-users list but you are willing
> >> >> >> to share it with the ChimeraX team, you can send it to just my
> >> >> >> individual e-mail address. However, if you need to keep it
> >> >> >> completely private we understand.
> >> >> >> > Best,
> >> >> >> > Elaine
> >> >> >> > -----
> >> >> >> > Elaine C. Meng, Ph.D.
> >> >> >> > UCSF Chimera(X) team
> >> >> >> > Department of Pharmaceutical Chemistry
> >> >> >> > University of California, San Francisco
> >> >> >> >
> >> >> >> >> On Mar 21, 2022, at 2:28 AM, Enrico Martinez
> >> >> >> <jmsstarlight at gmail.com> wrote:
> >> >> >> >>
> >> >> >> >> 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
> >> >> >> >>>>>>>
> >> >> >> >>>>>
> >> >> >> >>>>
> >> >> >> >>>>
> >> >> >> >>>> _______________________________________________
> >> >> >> >>>> ChimeraX-users mailing list
> >> >> >> >>>> ChimeraX-users at cgl.ucsf.edu
> >> >> >> >>>> Manage subscription:
> >> >> >> >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> >> >> >> >>>>
> >> >> >> >>>
> >> >> >> >> <test_hbonds-min.png>
> >> >> >> >
> >> >> >> >
> >> >> >> > _______________________________________________
> >> >> >> > ChimeraX-users mailing list
> >> >> >> > ChimeraX-users at cgl.ucsf.edu
> >> >> >> > Manage subscription:
> >> >> >> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> >> >> >> >
> >> >> >>
> >> >> >
> >> >> > _______________________________________________
> >> >> > ChimeraX-users mailing list
> >> >> > ChimeraX-users at cgl.ucsf.edu
> >> >> > Manage subscription:
> >> >> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> >> >>
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> ChimeraX-users mailing list
> >> >> ChimeraX-users at cgl.ucsf.edu
> >> >> Manage subscription:
> >> >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> >>
> >>
> >>
>
>
>
More information about the ChimeraX-users
mailing list