Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5117 closed defect (nonchimerax)

Modeller results disliked by Coot

Reported by: yen-li.li@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
I actually don't know if this is something related to Modeller or Chimera. I generated homology model using Modeller Comparative in Chimera X. I then input the pdb file of the model in Coot for model buidling in EM map. The model generated from modeller; however, showed bad geometry graph in Coot. The original pdb file used as a template for homology model building showed good geometry graph.  Do I need to save the homology model as specific format to carry some critical information or do some additional setting (not default)? I also tried ISOLDE in ChimeraX, which didn't show obvious geometry problem. 

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

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OpenGL version: 3.3.0 NVIDIA 471.68
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Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Home (Build 19042)
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File attachment: modeller model in coot.png

modeller model in coot.png​

Attachments (1)

modeller model in coot.png​ (57.2 KB ) - added by yen-li.li@… 4 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (5)

by yen-li.li@…, 4 years ago

Attachment: modeller model in coot.png​ added

Added by email2trac

in reply to:  2 comment:1 by Yen-Li.Li@…, 4 years ago 

Dear Chimera X team,

I tried other thing and found that if the model was built without hydrogen using modeller comparative, there is no error in geometry profile in Coot. It only happened when I included hydrogen. Is it common?

Best,
Yen-Li
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, August 27, 2021 11:37 AM
Cc: Li, Yen-Li <Yen-Li.Li@ucsf.edu>
Subject: Re: [ChimeraX] #5117: ChimeraX bug report submission

#5117: ChimeraX bug report submission
----------------------------------+--------------------
          Reporter:  yen-li.li@…  |      Owner:  (none)
              Type:  defect       |     Status:  new
          Priority:  normal       |  Milestone:
         Component:  Unassigned   |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |
----------------------------------+--------------------
Changes (by yen-li.li@…):

 * Attachment "modeller model in coot.png" added.

 Added by email2trac

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5117>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 4 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Modeller results disliked by Coot

comment:3 by Eric Pettersen, 4 years ago

Resolution: → nonchimerax
Status: accepted → closed

Hi Yen-Li,

ChimeraX merely makes it easy to prepare the inputs and run Modeller -- it show the results from Modeller unchanged. So if the results are problematic, you would have to ask about that on the Modeller mailing list (​https://salilab.org/mailman/listinfo/modeller_usage). If having Modeller add the hydrogens seems problematic, you could run Modeller without having it model hydrogens and then add hydrogens afterward with ChimeraX's "addh" command.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  5 comment:4 by Yen-Li.Li@…, 4 years ago 

Hi Eric,

Thank you for your help. I finally realized that it's neither modeller nor chimera issue. Even I just added hydrogen onto a pdb file downloaded from the PDB or AlphaFold database by typing "addh", the coot showed geometry error. I think I will contact ISOLDE or coot since ISOLDE needs hydrogen atoms to run the simulation.

Have a good weekend.
Yen-Li
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, August 27, 2021 3:42 PM
Cc: PETTERSEN, ERIC <pett@cgl.ucsf.edu>; Li, Yen-Li <Yen-Li.Li@ucsf.edu>
Subject: Re: [ChimeraX] #5117: Modeller results disliked by Coot

#5117: Modeller results disliked by Coot
----------------------------------+----------------------------
          Reporter:  yen-li.li@…  |      Owner:  Eric Pettersen
              Type:  defect       |     Status:  closed
          Priority:  normal       |  Milestone:
         Component:  Sequence     |    Version:
        Resolution:  nonchimerax  |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+----------------------------
Changes (by Eric Pettersen):

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


Comment:

 Hi Yen-Li,
         ChimeraX merely makes it easy to prepare the inputs and run
 Modeller -- it show the results from Modeller unchanged.  So if the
 results are problematic, you would have to ask about that on the Modeller
 mailing list (https://urldefense.com/v3/__https://salilab.org/mailman/listinfo/modeller_usage__;!!LQC6Cpwp!4PHGMSFJIA3v8LFzMiRtYPpA1e4OJVMuLkFgCjjM_l9E5xl89lvmVjrZNr1e_ab9vg$ ).  If
 having Modeller add the hydrogens seems problematic, you could run
 Modeller without having it model hydrogens and then add hydrogens
 afterward with ChimeraX's "addh" command.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5117#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
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