RFE: make ViewDockX understand SwissDock output

[Elaine Meng]

On Feb 9, 2021, at 3:56 AM, Michael Weber wrote:
... I use SwissDock for molecular docking experiments and there is an explanation on how to examine the output results in Chimera. Unfortunately all those workflows appear not to work in ChimeraX - are there any plans (or even already existing documentation which very well might have escaped my attention) to get these working in ChimeraX as well? Invoking ViewDockX from either the menu >tools>general>ViewDockX or by typing the command after having loaded a PDB structure plus the docked ligands just results in the message "No suitable models found for ViewDockX".

Elaine:
I was able to get a set of example results from the server. I see that the ligand PDB file just has all the positions strung together in one huge model (does not separate them into individual models). I tried manually editing to add MODEL and ENDMDL records so that they would be read as individual models (clusters-edited.pdb subset of results attached), which did work, but ViewDockX still does not recognize that set of models as docking results nor does it read the scores and other descriptors that are in the REMARK records. I guess the code would need to be modified to support SwissDock output.

Zip file of results from the SwissDock server <​http://swissdock.ch/> is attached. The resulting folder includes target.pdb (receptor) and clusters.dock4.pdb (different positions of a single ligand, basis for edited file mentioned above).

[weberm@…]

Hi,
I saw that there is a new ChimeraX release, has there been any progress 
on fixing the ViewDockX module to understand the SwissDock output files 
yet?

Best regards,
Michael.

Am 19.02.2021 00:51 schrieb ChimeraX:

[Elaine Meng]

Hi Michael,
Sorry no.  If there is progress on this ticket you would automatically get e-mail about it, I believe.  The original developer of that tool retired, and there are many open tickets, so I don't know the time frame.
Elaine

[pett]

Looks like Conrad (and summer students) made the somewhat ugly decision that ViewDockX identifies docking output by seeing if there is a “viewdockx_data” attribute in the structure (which has a bunch of information in it). The Mol2, PDBQT, and Maestro readers that he/they implemented all put that attribute into the resultant structure(s). The normal PDB reader of course does not, and these SwissDock output files are PDB files.

There are two possible approaches I can think of. One is to tell ChimeraX that this is SwissDock PDB output as you open it (i.e. open x.pdb format swissdock). The other is to have ViewDockX look at the open structures when it starts and see if any "look like" SwissDock output and try to create the viewdockx_data attribute on the fly. The first approach is easier to program and less error prone. The second approach is easier for the user but more error prone.

[weberm@…]

Just a short question: The ticket is >1 year old, are there plans to 
implement the suggested modifications? Is this a lot of work?
Best regards,
Michael.

Am 24.06.2022 02:22 schrieb ChimeraX:

[pett]

It's roughly a day's worth of work. There's a lot of priorities it's competing against.

[weberm@…]

Hi,
not sure whether this idea is of help, but in Chimera the SwissDock 
output files can be opened and visualized in ViewDock. What does not yet 
work is saving the Chimera situation as a project file that is then 
compatible to ChimeraX. If I noticed correctly, this output 
compatibility issue is also on your to do list, so maybe two problems 
could be solved at once?
I am really desperately waiting for the possibility to use ViewDockX in 
ChieraX wit SwissDock output files. ;-)
Best regards,
Michael.

Am 14.07.2022 21:20 schrieb ChimeraX:

[pett]

Will be available in the next daily build. You will have to open both receptor and ligands with the "format swissdock" arguments (e.g. "open receptor.pdb ligands.pdb format swissdock") or, if you are using the File→Open dialog, by switching from "All Files" to "SwissDock".

[luigi.marongiu@…]

Great, thank you!
Best regards
Luigi
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, February 3, 2023 03:05
Cc: fconsoli@usp.br <fconsoli@usp.br>; luigi.marongiu@outlook.com <luigi.marongiu@outlook.com>; meng@cgl.ucsf.edu <meng@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; weberm@posteo.de <weberm@posteo.de>
Subject: Re: [ChimeraX] #4232: RFE: make ViewDockX understand SwissDock output

#4232: RFE: make ViewDockX understand SwissDock output
-----------------------------------------------+--------------------
          Reporter:  Elaine Meng               |      Owner:  pett
              Type:  enhancement               |     Status:  closed
          Priority:  moderate                  |  Milestone:
         Component:  Surface/Binding Analysis  |    Version:
        Resolution:  fixed                     |   Keywords:
        Blocked By:                            |   Blocking:
Notify when closed:                            |   Platform:  all
           Project:  ChimeraX                  |
-----------------------------------------------+--------------------
Changes (by pett):

 * status:  accepted => closed
 * resolution:   => fixed


Comment:

 Will be available in the next daily build.  You will have to open both
 receptor and ligands with the "format swissdock" arguments (e.g. "open
 receptor.pdb ligands.pdb format swissdock") or, if you are using the
 File→Open dialog, by switching from "All Files" to "SwissDock".

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4232#comment:11>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[pett]

Sorry it took me so long to get to it. Let me know if you have any problems.