[chimerax-users] how to vizualise hydrogen bonds between ligand and back-bone of protein?
JAMES MICHAEL S1JJRUdFUiA=
jmkrieger at cnb.csic.es
Wed Mar 23 07:50:06 PDT 2022
Perfect! Thanks for the useful update too!
Enrico Martinez <jmsstarlight at gmail.com> escribió:
> Right, thank you James!
> Indeed the following script using pymol directly in bash could fix the
> issue with my pdb so the ChimeraX recognize all hydrogen bonds
> correctly!
>
> #!/usr/local/bin/bash
> home="$PWD"
> pdb="${home}"/input.pdb
>
> #run pymol in batch mode to fix the pdb
> pymol -c -d "
> from pymol import cmd
> cmd.load('$pdb')
> # execute some command to fix atom order in the multi-model pdb
> cmd.save('input_proc.pdb', state='0')
> "
>
> вт, 22 мар. 2022 г. в 18:04, JAMES MICHAEL S1JJRUdFUiA=
> <jmkrieger at cnb.csic.es>:
>>
>> No, sorry. It should be possible to run pymol with a script in that
>> way, but I've never actually done it.
>> Best wishes
>> James
>>
>> Enrico Martinez <jmsstarlight at gmail.com> escribió:
>>
>> > 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
>> >> >>
>> >> >>
>> >> >>
>> >>
>> >>
>> >>
>>
>>
>>
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