Maestro file not recognized by ViewdockX

[Elaine Meng]

From: "Rangarajan, Amith via ChimeraX-users" <chimerax-users@…>
Subject: Re: [chimerax-users] No suitable models found for viewDockX
Date: February 20, 2022 at 3:51:36 PM PST

hello chimeraX,
I am trying to open a glide docking result using viewdockx and i am getting this error message ('no suitable models found").

I tried opening the file as .mae file ( protein and ligand are both in same model )and a pv.mae file ( protein and ligand are in diff models). I am still getting the same error.

From: "Rangarajan, Amith" <Amith.Rangarajan@…>
Subject: Re: [chimerax-users] No suitable models found for viewDockX
Date: February 22, 2022 at 12:25:10 PM PST

Hi elaine,
Thanks for the response. Please see the files in attachment.

test-pv.mae : it contains protein and ligand as seperate entries and it is a poseviewer file.
test-pv_arom-IFD_CHEMBL1271655.mae : this a mae file which as both protein and ligand as a single entry

I made a session of chimerax 1.3 with both these files and ran viewdock command.
I tried viewdockx on both these files separately in a chimera session, and i am getting the same error.
please let me know what will fix this issue.
I am using a windows machine.
thanks
amith

[example files from Amith attached]

Elaine: the poseviewer one is more likely to work because it is more similar to the example file I have that does work. However, I can reproduce the same error message you reported when I try it.

[Elaine Meng]

oops I forgot attaching would put them in the public database... now I've deleted the attachments and will send to Eric privately instead.

[Amith.Rangarajan@…]

dear Meng,Eric.

I tried viewdockx command with the attached poseviewer file and it works perfectly.

i think viewdocx program is picky about the mae file format.

The earlier file that i sent which did not open was   created  by combining receptor and ligand together , it was not the direct output from glide docking.

I dont understand the nuances of mae file formats enough to explain it. but i hope the attached file ( which opens in viewdockx and is a direct output of glide docking) might help you debug it .

i think something in view doc x documentation can be updated to this effect.

thanks
amith
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, February 22, 2022 12:54 PM
Cc: Rangarajan, Amith <Amith.Rangarajan@ucsf.edu>; Elaine Meng <meng@cgl.ucsf.edu>; PETTERSEN, ERIC <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #6226: Maestro file not recognized by ViewdockX

#6226: Maestro file not recognized by ViewdockX
-----------------------------------------------+----------------------
          Reporter:  Elaine Meng               |      Owner:  pett
              Type:  defect                    |     Status:  assigned
          Priority:  high                      |  Milestone:
         Component:  Surface/Binding Analysis  |    Version:
        Resolution:                            |   Keywords:
        Blocked By:                            |   Blocking:
Notify when closed:                            |   Platform:  all
           Project:  ChimeraX                  |
-----------------------------------------------+----------------------

Comment (by Elaine Meng):

 oops I forgot attaching would put them in the public database... now I've
 deleted the attachments and will send to Eric privately instead.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6226#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

vsw_epik_non-substrates-XP_OUT_1_pv.maegz​

[Amith.Rangarajan@…]

Added by email2trac

[Elaine Meng]

Hi Amith,
To clarify:  do you mean that to prevent these errors, we can just add something to the ViewDockX documentation like "this should be the .mae or .maegz file output directly by Glide, not processed to combine receptor and ligand" ? 

We don't use Glide/Maestro ourselves, so we need to know how to explain this issue to users so that they won't experience the problem.  For example, I never heard the term "poseviewer" before until you said it in your message... is that Glide terminology, and do you think it would be helpful to include that word in the documentation?  

Thanks for any thoughts on how to explain it clearly,
Elaine

[Eric Pettersen]

For ViewDockX to show results, the .mae or .maegz files have to have "r_i_docking_score" attributes in them. Neither of the files that didn't work have those attributes. The file that did work has them.