O1P/O2P disconnected

[nicholas.sofos@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-22)
Description
I have a few models containing RNA duplexes, where the two phosphate oxygens O1P and O2P are displayed as free atoms, and not covalently linked to the phosphorous atom. When displaying the same model in Chimera (v. 1.13.1 build 41949) I don't have this problem, and when I save the .pdb in Chimera and re-open it in ChimeraX, the model is displayed correctly. However, I prefer to not have to open and save all my models in Chimera before displaying them in ChimeraX.

OpenGL version: 4.1 INTEL-12.4.7
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Eric Pettersen]

Hi Nicolas,

Is the original file with the O1P/O2P problem in mmCIF format or PDB format?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[nicholas.sofos@…]

Hi Eric,

It's in pdb.

23. apr. 2019 19.36 skrev ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>:
#1884: O1P/O2P disconnected
---------------------------------------+----------------------
          Reporter:  nicholas.sofos@…  |      Owner:  pett
              Type:  defect            |     Status:  accepted
          Priority:  normal            |  Milestone:
         Component:  Input/Output      |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+----------------------
Changes (by pett):

 * status:  new => accepted
 * cc: gregc (added)
 * component:  Unassigned => Input/Output
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => pett


Comment:

 Hi Nicolas,
         Is the original file with the O1P/O2P problem in mmCIF format or
 PDB format?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1884#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Opening regular RNA PDB files (e.g. 3gx2) works fine, so it would help me if you could attach an example file. It needn't be the entire structure if that's a problem, just the part that's problematic.

--Eric

[nicholas.sofos@…]

Yes, I also found several examples where the RNA is displayed fine. An example where it fails is attached.

Best
Nicholas

On 23/04/2019, 21.25, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #1884: O1P/O2P disconnected
    ---------------------------------------+----------------------
              Reporter:  nicholas.sofos@…  |      Owner:  pett
                  Type:  defect            |     Status:  feedback
              Priority:  normal            |  Milestone:
             Component:  Input/Output      |    Version:
            Resolution:                    |   Keywords:
            Blocked By:                    |   Blocking:
    Notify when closed:                    |   Platform:  all
               Project:  ChimeraX          |
    ---------------------------------------+----------------------
    
    Comment (by pett):
    
     Opening regular RNA PDB files (e.g. 3gx2) works fine, so it would help me
     if you could attach an example file.  It needn't be the entire structure
     if that's a problem, just the part that's problematic.
    
     --Eric
    
    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1884#comment:4>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker
    

RNAdup1.pdb​

[nicholas.sofos@…]

Added by email2trac

[Eric Pettersen]

Thanks, I can reproduce the problem now!

--Eric

[Eric Pettersen]

An "efficiency" change made awhile back also changed the logic incorrectly.