[chimerax-users] Analysis of the protein-ligand interactions using ViewDock
Enrico Martinez
jmsstarlight at gmail.com
Mon Mar 7 07:01:47 PST 2022
some update:
actually I've tried it with my multi model pdb adding coordsets true:
hbonds #1 & ligand coordsets true interModel false makePseudobonds
false log true intraRes false saveFile total_hbonds.log
and finally what I may see in the output log is a kind of fusion
between al detected h-bonds in each of the separated frame:
Models used:
1.1 06I_nsp5holo_rep1.pdb
1.2 06I_nsp5holo_rep1.pdb
1.3 06I_nsp5holo_rep1.pdb
1.4 06I_nsp5holo_rep1.pdb
1.5 06I_nsp5holo_rep1.pdb
1.6 06I_nsp5holo_rep1.pdb
1.7 06I_nsp5holo_rep1.pdb
1.8 06I_nsp5holo_rep1.pdb
1.9 06I_nsp5holo_rep1.pdb
1.10 06I_nsp5holo_rep1.pdb
1.11 06I_nsp5holo_rep1.pdb
1.12 06I_nsp5holo_rep1.pdb
1.13 06I_nsp5holo_rep1.pdb
1.14 06I_nsp5holo_rep1.pdb
1.15 06I_nsp5holo_rep1.pdb
1.16 06I_nsp5holo_rep1.pdb
1.17 06I_nsp5holo_rep1.pdb
1.18 06I_nsp5holo_rep1.pdb
1.19 06I_nsp5holo_rep1.pdb
1.20 06I_nsp5holo_rep1.pdb
1.21 06I_nsp5holo_rep1.pdb
1.22 06I_nsp5holo_rep1.pdb
1.23 06I_nsp5holo_rep1.pdb
1.24 06I_nsp5holo_rep1.pdb
1.25 06I_nsp5holo_rep1.pdb
1.26 06I_nsp5holo_rep1.pdb
1.27 06I_nsp5holo_rep1.pdb
1.28 06I_nsp5holo_rep1.pdb
1.29 06I_nsp5holo_rep1.pdb
1.30 06I_nsp5holo_rep1.pdb
1.31 06I_nsp5holo_rep1.pdb
49 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
06I_nsp5holo_rep1.pdb #1.1/? THR 26 N 06I_nsp5holo_rep1.pdb
#1.1/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.1/? THR 26 H 3.515
2.716
06I_nsp5holo_rep1.pdb #1.1/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.1/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.1/? ASN 142 2HD2 3.227
2.305
06I_nsp5holo_rep1.pdb #1.1/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.1/? THR 26 O 06I_nsp5holo_rep1.pdb #1.1/A UNL 1 H 3.463
2.652
06I_nsp5holo_rep1.pdb #1.2/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.2/? PHE 140 O 06I_nsp5holo_rep1.pdb #1.2/A UNL 1 H 2.987
2.200
06I_nsp5holo_rep1.pdb #1.4/? THR 26 N 06I_nsp5holo_rep1.pdb
#1.4/A UNL 1 S 06I_nsp5holo_rep1.pdb #1.4/? THR 26 H 4.354
3.371
06I_nsp5holo_rep1.pdb #1.4/? HIS 163 NE2 06I_nsp5holo_rep1.pdb
#1.4/A UNL 1 N no hydrogen
3.137 N/A
06I_nsp5holo_rep1.pdb #1.4/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.4/? ARG 188 O 06I_nsp5holo_rep1.pdb #1.4/A UNL 1 H 3.000
2.081
06I_nsp5holo_rep1.pdb #1.5/? HIS 163 NE2 06I_nsp5holo_rep1.pdb
#1.5/A UNL 1 N no hydrogen
3.330 N/A
06I_nsp5holo_rep1.pdb #1.5/? GLN 189 NE2 06I_nsp5holo_rep1.pdb
#1.5/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.5/? GLN 189 2HE2 3.029
2.132
06I_nsp5holo_rep1.pdb #1.6/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.6/? ARG 188 O 06I_nsp5holo_rep1.pdb #1.6/A UNL 1 H 2.984
2.064
06I_nsp5holo_rep1.pdb #1.8/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.8/A UNL 1 N 06I_nsp5holo_rep1.pdb #1.8/? ASN 142 2HD2 3.164
2.395
06I_nsp5holo_rep1.pdb #1.8/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.8/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.8/? ASN 142 2HD2 3.031
2.180
06I_nsp5holo_rep1.pdb #1.8/? GLN 189 NE2 06I_nsp5holo_rep1.pdb
#1.8/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.8/? GLN 189 1HE2 3.276
2.553
06I_nsp5holo_rep1.pdb #1.8/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.8/? THR 190 O 06I_nsp5holo_rep1.pdb #1.8/A UNL 1 H 3.257
2.407
06I_nsp5holo_rep1.pdb #1.9/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.9/? THR 190 O 06I_nsp5holo_rep1.pdb #1.9/A UNL 1 H 2.913
2.037
06I_nsp5holo_rep1.pdb #1.10/? SER 144 OG 06I_nsp5holo_rep1.pdb
#1.10/A UNL 1 S 06I_nsp5holo_rep1.pdb #1.10/? SER 144 HG 4.246
3.845
06I_nsp5holo_rep1.pdb #1.10/? HIS 163 NE2 06I_nsp5holo_rep1.pdb
#1.10/A UNL 1 S no hydrogen
3.700 N/A
06I_nsp5holo_rep1.pdb #1.10/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.10/? THR 190 O 06I_nsp5holo_rep1.pdb #1.10/A UNL 1 H 3.008
2.091
06I_nsp5holo_rep1.pdb #1.12/? GLN 189 NE2 06I_nsp5holo_rep1.pdb
#1.12/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.12/? GLN 189 1HE2 2.929
2.152
06I_nsp5holo_rep1.pdb #1.12/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.12/? PHE 140 O 06I_nsp5holo_rep1.pdb #1.12/A UNL 1 H 2.912
2.012
06I_nsp5holo_rep1.pdb #1.13/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.13/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.13/? ASN 142 2HD2 3.063
2.291
06I_nsp5holo_rep1.pdb #1.14/? HIS 41 NE2 06I_nsp5holo_rep1.pdb
#1.14/A UNL 1 S no hydrogen
3.919 N/A
06I_nsp5holo_rep1.pdb #1.14/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.14/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.14/? ASN 142 2HD2 2.802
1.872
06I_nsp5holo_rep1.pdb #1.14/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.14/? THR 190 O 06I_nsp5holo_rep1.pdb #1.14/A UNL 1 H 2.927
1.987
06I_nsp5holo_rep1.pdb #1.16/? GLN 189 NE2 06I_nsp5holo_rep1.pdb
#1.16/A UNL 1 N 06I_nsp5holo_rep1.pdb #1.16/? GLN 189 1HE2 3.456
2.669
06I_nsp5holo_rep1.pdb #1.16/? GLN 189 NE2 06I_nsp5holo_rep1.pdb
#1.16/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.16/? GLN 189 1HE2 3.079
2.177
06I_nsp5holo_rep1.pdb #1.16/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.16/? THR 190 O 06I_nsp5holo_rep1.pdb #1.16/A UNL 1 H 2.967
1.987
06I_nsp5holo_rep1.pdb #1.17/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.17/A UNL 1 N 06I_nsp5holo_rep1.pdb #1.17/? ASN 142 2HD2 3.218
2.294
06I_nsp5holo_rep1.pdb #1.17/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.17/? THR 190 O 06I_nsp5holo_rep1.pdb #1.17/A UNL 1 H 3.364
2.469
06I_nsp5holo_rep1.pdb #1.18/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.18/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.18/? ASN 142 2HD2 3.117
2.142
06I_nsp5holo_rep1.pdb #1.20/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.20/A UNL 1 N 06I_nsp5holo_rep1.pdb #1.20/? ASN 142 2HD2 3.245
2.560
06I_nsp5holo_rep1.pdb #1.21/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.21/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.21/? ASN 142 2HD2 3.033
2.423
06I_nsp5holo_rep1.pdb #1.21/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.21/? ARG 188 O 06I_nsp5holo_rep1.pdb #1.21/A UNL 1 H 3.157
2.238
06I_nsp5holo_rep1.pdb #1.22/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.22/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.22/? ASN 142 2HD2 3.035
2.130
06I_nsp5holo_rep1.pdb #1.23/? THR 26 N 06I_nsp5holo_rep1.pdb
#1.23/A UNL 1 S 06I_nsp5holo_rep1.pdb #1.23/? THR 26 H 4.011
2.970
06I_nsp5holo_rep1.pdb #1.23/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.23/? GLU 166 OE1 06I_nsp5holo_rep1.pdb #1.23/A UNL 1 H 3.151
2.261
06I_nsp5holo_rep1.pdb #1.24/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.24/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.24/? ASN 142 2HD2 3.200
2.518
06I_nsp5holo_rep1.pdb #1.25/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.25/A UNL 1 N 06I_nsp5holo_rep1.pdb #1.25/? ASN 142 2HD2 3.361
2.626
06I_nsp5holo_rep1.pdb #1.25/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.25/? THR 190 O 06I_nsp5holo_rep1.pdb #1.25/A UNL 1 H 3.213
2.296
06I_nsp5holo_rep1.pdb #1.26/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.26/? HIS 41 NE2 06I_nsp5holo_rep1.pdb #1.26/A UNL 1 H 3.118
2.288
06I_nsp5holo_rep1.pdb #1.27/? GLN 189 NE2 06I_nsp5holo_rep1.pdb
#1.27/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.27/? GLN 189 1HE2 3.023
2.403
06I_nsp5holo_rep1.pdb #1.27/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.27/? PHE 140 O 06I_nsp5holo_rep1.pdb #1.27/A UNL 1 H 2.875
2.036
06I_nsp5holo_rep1.pdb #1.28/? GLY 143 N 06I_nsp5holo_rep1.pdb
#1.28/A UNL 1 S 06I_nsp5holo_rep1.pdb #1.28/? GLY 143 H 3.738
2.860
06I_nsp5holo_rep1.pdb #1.28/? CYS 145 SG 06I_nsp5holo_rep1.pdb
#1.28/A UNL 1 S 06I_nsp5holo_rep1.pdb #1.28/? CYS 145 HG 3.827
2.830
06I_nsp5holo_rep1.pdb #1.29/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.29/? PHE 140 O 06I_nsp5holo_rep1.pdb #1.29/A UNL 1 H 2.937
2.019
06I_nsp5holo_rep1.pdb #1.30/? ASN 142 ND2 06I_nsp5holo_rep1.pdb
#1.30/A UNL 1 O 06I_nsp5holo_rep1.pdb #1.30/? ASN 142 2HD2 3.041
2.335
06I_nsp5holo_rep1.pdb #1.31/? HIS 163 NE2 06I_nsp5holo_rep1.pdb
#1.31/A UNL 1 O no hydrogen
3.090 N/A
06I_nsp5holo_rep1.pdb #1.31/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.31/? PHE 140 O 06I_nsp5holo_rep1.pdb #1.31/A UNL 1 H 3.450
2.641
06I_nsp5holo_rep1.pdb #1.31/A UNL 1 N 06I_nsp5holo_rep1.pdb
#1.31/? HIS 163 NE2 06I_nsp5holo_rep1.pdb #1.31/A UNL 1 H 3.264
2.532
If the command is correct, may it be possible to reorder the info
according to each individual mode?
For instance, just taking the first frame from this ensemble
(corresponded to #1.1), I have been able to obtain something like
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? THR 26 N /A UNL 1 O /? THR 26 H 3.515 2.716
/? ASN 142 ND2 /A UNL 1 O /? ASN 142 2HD2 3.227 2.305
/A UNL 1 N /? THR 26 O /A UNL 1 H 3.463 2.652
would it be possible to do it for multi-model pdb as well ?
Cheers
Enrico
пн, 7 мар. 2022 г. в 15:07, Enrico Martinez <jmsstarlight at gmail.com>:
>
> Thank you very much Elaine!
> Indeed I forgot to precise the output in the multi-model pdb where
> both protein and ligand are present in each frame. So the frames are
> different according to the predicted pose.
> I have already used ChimeraX for the printing info regarding H bonds
> in this format, BUT considering only the first model from the pdb.
> Here is my script :
>
> open complex.pdb
> close #1.2-end # keeping only the first model
> view
> wait
> #Visualisation of the h-bonds between ligand and protein
> hbonds #1.1 & ligand reveal true log true radius 0.06 dashes 6 color
> turquoise twoColors true slopColor indigo intraRes false saveFile
> hbonds.log
>
> Here are my questions:
> 1) may I adapt it to check the H-bonds in the multi-model pdb (via
> sleeping close #1.2-end)?
> I suppose I will need to add there : intraModel false, intraMol false
> 2)May I add additionally in my workflow the command clashes | contacts
> to save info regarding other contacts detected in each frame ?
>
> Cheers,
> Enrico
>
> пт, 4 мар. 2022 г. в 17:51, Elaine Meng <meng at cgl.ucsf.edu>:
> >
> > Hello,
> > You will need to actually try the steps yourself to work out the protocol, but I can give you a few pointers. First (before trying to write a script) you should just use trial and error of typing commands directly into the command line yourself to figure out what they should be.
> >
> > (1) of course you can open the receptor PDB, command "open"
> > ...for local file
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local>
> > ...or fetch from PDB
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch>
> >
> > (2) I don't know what format your docked ligands are in. ChimeraX tool ViewDockX knows some but not all of the same formats that Chimera knows. Since what you describe is showing all of the docked ligands together at the same time, it may not be necessary to use the ViewDockX tool. If you don't use it, however, you would still need to use some format that ChimeraX knows how to read.
> > You would use the "open" command if it is a file that ChimeraX can read. If not, you would have to keep using Chimera.
> >
> > ViewDockX formats
> > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>
> >
> > atomic structure formats known to ChimeraX in general
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic>
> >
> > (3) then if you can actually open the docked ligands, you can see in the Model Panel (when you are trying this interactively) what their model number(s) are, to later use in commands in your script. If you are using a command to find hbonds, you don't need to select the ligands, however -- you can specify them directly in the hbonds command.
> >
> > (4) ChimeraX and Chimera both have commands to find H-bonds. In ChimeraX the command is "hbonds" and you can specify the docked ligand model(s) directly, e.g. if they are all in #2, "hbonds #2 restrict any reveal true saveFile myoutputfile.txt" -- but please read the help to see what options you want:
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html>
> >
> > Another way in ChimeraX to figure out the hbonds command is to use the H-Bonds graphical interface: menu: Tools... Structure Analysis... H-Bonds. Then when you click OK or Apply, the corresponding command will be shown in the Log. One difference, however, is that if using the GUI you would need to select the ligands first (which can be done with the Model panel checkboxes under the selecting-hand icon, or command like "select #2") whereas the "hbonds" command allows simply specifying them in the command, as in my example command above.
> >
> > I cannot overemphasize, however, that you should not expect to write a script, or have somebody just give you a script and have the whole thing work right away -- most experts can't even do that, including me -- instead you really need to try the commands interactively on your specific data and see what works before putting them in a script.
> >
> > 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 4, 2022, at 8:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > >
> > > Dear ChimeraX users!
> > >
> > > I would like to use ChimeraX to calculate protein-ligand contacts
> > > established in docking calculations for the ensemble of the docking
> > > solutions (88 conformations of the ligand saved in multi-model
> > > format). Basically using the GUI of the UCSF Chimera previously I
> > > could do the following routine for the analysis of docking results:
> > > 1. Open the protein PDB
> > > 2. Use the Surface/Binding Analysis > ViewDock tool to open the docking poses
> > > 3. Using the Model Panel, select all docking poses
> > > 4. Use the Surface/Binding Analysis > FindHBond tool to locate all
> > > H-bonds. Make sure to check "Only find H-bonds with at least 1 end
> > > selected". You can check "write information to file" to save the
> > > H-bonds.
> > >
> > > May I adapt this protocol with the ChimeraX to perform such computing
> > > in batch (no-gui mode)? What should be the differences in the commands
> > > between Chimera and ChimeraX ( I've already seen that ViewDock is
> > > available in the ChimeraX as well...)
> > > Many thanks in advance!
> > > Cheers
> > > Enrico
> > > _
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