Issue opening pdb files from ZDOCK

[shawn.owen@…]

Hi,
I haven't used ZDOCK in a while but ran some predictions to compare with other platforms. Itried to open the pdb files that the program generated. None of them will open on ChimeraX version 1.5 (2022-11-24).
Any thoughts?
For each of the files, I get an error:
[cid:1a4c1acb-08a0-41c8-9758-29b96060a786]
I've attached one of the files in case that helps.

Much appreciated!!
Shawn

complex.1.pdb​

[shawn.owen@…]

Added by email2trac

[shawn.owen@…]

Added by email2trac

[pett]

Hi Shawn,

The ZDOCK "PDB" file does not conform to the PDB standard and cannot be read by ChimeraX's normal PDB reader. You have to inform ChimeraX that the format is ZDOCK so that it uses a special-purpose ZDOCK reader. You this either by adding "format zdock" to your open command or, if you are using the File→Open dialog, by changing the file type menu to "ZDOCK".

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[shawn.owen@…]

Eric - thanks a lot!
Such an easy fix, sorry to bug you with it. I'm such a noob.

Much appreciated,
Shawn
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, February 21, 2023 11:11 AM
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Shawn Owen <shawn.owen@hsc.utah.edu>
Subject: Re: [ChimeraX] #8533: Issue opening pdb files from ZDOCK

#8533: Issue opening pdb files from ZDOCK
-----------------------------------+--------------------
          Reporter:  shawn.owen@…  |      Owner:  pett
              Type:  defect        |     Status:  closed
          Priority:  normal        |  Milestone:
         Component:  Input/Output  |    Version:
        Resolution:  duplicate     |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+--------------------
Changes (by pett):

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


Comment:

 Hi Shawn,
         The ZDOCK "PDB" file does not conform to the PDB standard and
 cannot be read by ChimeraX's normal PDB reader.  You have to inform
 ChimeraX that the format is ZDOCK so that it uses a special-purpose ZDOCK
 reader.  You this either by adding "format zdock" to your open command or,
 if you are using the File→Open dialog, by changing the file type menu to
 "ZDOCK".

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8533#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[pett]

No prob -- it's easy to forget these things.