Missing bond

[juha.vahokoski@…]

The following bug report has been submitted:
Platform:        Windows-7-6.1.7601-SP1
ChimeraX Version: 0.9 (2019-02-19)
Description
Does not show a covalent bond between O1B and Pb, when a link record is present (LINK        MG    MG B 401                 O1B ADP B 400).

OpenGL version: 3.3.0 - Build 20.19.15.4454
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel
File attachment: link.png

link.png​

[juha.vahokoski@…]

Added by email2trac

[Eric Pettersen]

Hi Juha,

Is this a standard PDB entry? If so, what is the entry code? If not, can you provide the PDB file?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Juha.Vahokoski@…]

It is indeed some kind of annotation problem, what is popping up in my phenix.real_space_refinement/coot files. I checked a few similar structures out the PDB, and they do not exhibit the same problem.

I attached the offending piece of coordinates, without protein atoms off-course.

Regards,
Juha

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, February 19, 2019 8:28 PM
Cc: Juha Vahokoski <Juha.Vahokoski@uib.no>; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #1716: Missing bond

#1716: Missing bond
---------------------------------------+----------------------
          Reporter:  juha.vahokoski@…  |      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          |
---------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 Hi Juha,
         Is this a standard PDB entry?  If so, what is the entry code?  If
 not, can you provide the PDB file?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1716#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

chainB_edit.pdb​

[Juha.Vahokoski@…]

Added by email2trac

[Eric Pettersen]

Hi Juha,

I understand the problem. In a standard PDB entry there would be CONECT records for the ADP and that is why similar structures from the PDB look correct (the CONECT records contain the oxygen's other bond). Chimera(X) looks at your structure and connects up the atoms with no CONECT/LINK records based on distance. Unfortunately, the problematic oxygen *does* have a LINK record, so Chimera skips it, believing that its connectivity has been completely specified by CONECT/LINK records when in fact it hasn't. I can fix this, but it might be a little while before I get to it.
In the interim, is there any way you can force Phenix/Coot to output CONECT records for the ADP?

--Eric

[Juha.Vahokoski@…]

I think the root of the problem is that coot ignores CONECT records. When I know the behaviour, it easy enough to fix by manually adding numbers.

Thanks,
Juha

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, February 19, 2019 11:01 PM
Cc: Juha Vahokoski <Juha.Vahokoski@uib.no>; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #1716: Missing bond

#1716: Missing bond
---------------------------------------+----------------------
          Reporter:  juha.vahokoski@…  |      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:  feedback => accepted


Comment:

 Hi Juha,
         I understand the problem.  In a standard PDB entry there would be
 CONECT records for the ADP and that is why similar structures from the PDB
 look correct (the CONECT records contain the oxygen's other bond).
 Chimera(X) looks at your structure and connects up the atoms with no
 CONECT/LINK records based on distance.  Unfortunately, the problematic
 oxygen *does* have a LINK record, so Chimera skips it, believing that its
 connectivity has been completely specified by CONECT/LINK records when in
 fact it hasn't.  I can fix this, but it might be a little while before I
 get to it.
         In the interim, is there any way you can force Phenix/Coot to
 output CONECT records for the ADP?

 --Eric

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1716#comment:4>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

LINK/SSBOND now not treated as specifying all the connectivity of the involved atoms