PAE data not opened

[frauenstein@…]

Dear ChimeraX team,
I used the alpha fold prediction to align two interacting proteins and wanted to highlight the predicted aligned errors as described by the YouTube video. Even though I opened the alphafold predicted aligned error for the prediction of interest, Chimera X gives me the error message "Structure best model does not have PAE data opened" when invoking the command alphafold contacts /A to /B distance 8.
Thanks for helping,
Annika

[Eric Pettersen]

Reported by Annika Frauenstein

[Tom Goddard]

Hi Annika,

If you had more than one structure open, possibly you opened the PAE data for one structure but then used the "alphafold contacts" command on the other structure. If you have two structures open you will need to use a command like "alphafold #1/A to #1/B distance 8" and not "alphafold /A to /B distance 8". In other words you need to specify the model number (shown in the Models panel in ChimeraX, the first open structure is model #1, the second is #2, ...), otherwise the command tries to operate on all models with chain /A and /B.

Tom

[frauenstein@…]

Dear Tom,

Thanks for your reply. This unfortunately doesn't solve the problem (see screenshot). ChimeraX still doesn't recognize the loaded PAE data. I also only have one opened structure.

Thanks for your help.
Best,
Annika



-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Monday, July 25, 2022 11:01 PM
Cc: Frauenstein, Annika <frauenstein@biochem.mpg.de>; goddard@cgl.ucsf.edu
Subject: Re: [ChimeraX] #7322: PAE data not opened

#7322: PAE data not opened
-------------------------------------------+-------------------------
          Reporter:  frauenstein@…         |      Owner:  Tom Goddard
              Type:  defect                |     Status:  assigned
          Priority:  normal                |  Milestone:
         Component:  Structure Prediction  |    Version:
        Resolution:                        |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+-------------------------

Comment (by Tom Goddard):

 Hi Annika,

   If you had more than one structure open, possibly you opened the PAE  data for one structure but then used the "alphafold contacts" command on  the other structure.  If you have two structures open you will need to use  a command like "alphafold #1/A to #1/B distance 8"  and not "alphafold /A  to /B distance 8".  In other words you need to specify the model number  (shown in the Models panel in ChimeraX, the first open structure is model  #1, the second is #2, ...), otherwise the command tries to operate on all  models with chain /A and /B.

   Tom

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7322#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

Chimera X error 1.PNG​

[frauenstein@…]

Added by email2trac

[Tom Goddard]

Ok. Could you make a screen capture showing the entire ChimeraX window and the PAE plot window?

[Tom Goddard]

Fixed.

I finally figured this out. A change to ChimeraX on July 8 to allow opening PAE data even after residues were deleted inadvertently broke assigning PAE data to a structure. So all daily builds July 8 - August 2 were broken.