ISOLDE: assigned geometry mismatch

[valeriia.kalienkova@…]

The following bug report has been submitted:
Platform:        macOS-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.6rc202304072249 (2023-04-07 22:49:08 UTC)
Description
Hello! :)

I'm keen to try isolde for some of my structures, in this particular example I have cGMP bound. I was trying to modify it to template (MC-PCG), but there is some error (please find the screenshot attached). 

Hope this helps, thanks in advance! 

Cheers,
Valeria

Log:
UCSF ChimeraX version: 1.6rc202304072249 (2023-04-07)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> "/Users/valeriakalienkova/Library/CloudStorage/GoogleDrive-v.kalienkova@rug.nl/My
> Drive/structure/2N2_cGMP/230117_cGMP-bound_to_job112-coot-0.pdb" format pdb

Summary of feedback from opening
/Users/valeriakalienkova/Library/CloudStorage/GoogleDrive-v.kalienkova@rug.nl/My
Drive/structure/2N2_cGMP/230117_cGMP-bound_to_job112-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 57 57 HIS B
71 HIS B 73 1 3  
Start residue of secondary structure not found: HELIX 58 58 PHE B 80 SER B 93
1 14  
Start residue of secondary structure not found: HELIX 59 59 PRO B 121 GLU B
125 1 5  
Start residue of secondary structure not found: HELIX 60 60 PRO B 135 VAL B
137 1 3  
Start residue of secondary structure not found: HELIX 61 61 THR B 286 PHE B
289 1 4  
17 messages similar to the above omitted  
  
Chain information for 230117_cGMP-bound_to_job112-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> "/Users/valeriakalienkova/Library/CloudStorage/GoogleDrive-v.kalienkova@rug.nl/My
> Drive/structure/2N2_cGMP/relion_misc/job112/j112_wideTarget_3.mrc"

Opened j112_wideTarget_3.mrc as #2, grid size 300,300,300, pixel 1.02, shown
at level 0.00079, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.0672

> isolde start

> set selectionWidth 4

Populating font family aliases took 132 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 66 residues in model #1 to IUPAC-IUB
standards.  
Chain information for 230117_cGMP-bound_to_job112-coot-0.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> clipper associate #2 toModel #1

Opened j112_wideTarget_3.mrc as #1.1.1.1, grid size 300,300,300, pixel 1.02,
shown at step 1, values float32  

> isolde sim start sel

Loading residue template for PCG from internal database  
Sim termination reason: None  
ISOLDE: stopped sim  
Deleted the following atoms from residue GLU A1030: OE2  
Failed to add atoms ['H23'] to atom N2 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_PCG). If this template is
built into ISOLDE, please report this using Help/Report a bug  

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  
Failed to add atoms ['H23'] to atom N2 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_PCG). If this template is
built into ISOLDE, please report this using Help/Report a bug  

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  
Failed to add atoms ['H23'] to atom N2 because this will lead to having 4
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_PCG). If this template is
built into ISOLDE, please report this using Help/Report a bug  
[Repeated 1 time(s)]




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,9
      Model Number: Z17G003HRH/A
      Chip: Apple M2 Pro
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 4 hours, 43 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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File attachment: Screenshot 2023-04-11 at 00.09.49.png

Screenshot 2023-04-11 at 00.09.49.png​

[valeriia.kalienkova@…]

Added by email2trac

[Tristan Croll]

Thanks for reporting this! Unfortunately that set of residue parameters
(generated by an automated pipeline put together by Nigel Moriarty and
David Case) still contains a few errors like this, with nitrogens
incorrectly identified as amines. To get around it for now, first
double-check that the hydrogens on the residue are correct, then select it
and do “isolde param sel override true”. That should get it working for the
duration of your current session, and also save a {residue name}.xml file
in your current working directory (ChimeraX starts in the Desktop directory
by default). If you load that using ISOLDE’s Residue Parameterisation
widget in future sessions, you can skip the need to re-run the “isolde
param” command.

On Tue, 11 Apr 2023 at 17:21, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[valeriia.kalienkova@…]

Thanks a lot for your quick response, will try that!

Cheers,
Valeria
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 11 April 2023 18:31
To: tcroll@altoslabs.com <tcroll@altoslabs.com>; Valeriia Kalienkova <valeriia.kalienkova@uib.no>
Subject: Re: [ChimeraX] #8814: ISOLDE: assigned geometry mismatch

#8814: ISOLDE: assigned geometry mismatch
--------------------------------------------+---------------------------
          Reporter:  valeriia.kalienkova@…  |      Owner:  Tristan Croll
              Type:  defect                 |     Status:  assigned
          Priority:  normal                 |  Milestone:
         Component:  Third Party            |    Version:
        Resolution:                         |   Keywords:
        Blocked By:                         |   Blocking:
Notify when closed:                         |   Platform:  all
           Project:  ChimeraX               |
--------------------------------------------+---------------------------

Comment (by Tristan Croll):

 {{{
 Thanks for reporting this! Unfortunately that set of residue parameters
 (generated by an automated pipeline put together by Nigel Moriarty and
 David Case) still contains a few errors like this, with nitrogens
 incorrectly identified as amines. To get around it for now, first
 double-check that the hydrogens on the residue are correct, then select it
 and do “isolde param sel override true”. That should get it working for
 the
 duration of your current session, and also save a {residue name}.xml file
 in your current working directory (ChimeraX starts in the Desktop
 directory
 by default). If you load that using ISOLDE’s Residue Parameterisation
 widget in future sessions, you can skip the need to re-run the “isolde
 param” command.

 On Tue, 11 Apr 2023 at 17:21, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 wrote:

 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8814#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tristan Croll]

I take it this is working for you now? I'm afraid I was a bit slack and didn't get the corrected template into the ISOLDE 1.6 release, but it's committed now.

[valeriia.kalienkova@…]

Sorry I'm only replying now, but yes, it's working! Thanks a lot for your help - love Isolde!

cheers,
Valeria
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 14 June 2023 11:51
To: tcroll@altoslabs.com <tcroll@altoslabs.com>; Valeriia Kalienkova <valeriia.kalienkova@uib.no>
Subject: Re: [ChimeraX] #8814: ISOLDE: assigned geometry mismatch

#8814: ISOLDE: assigned geometry mismatch
--------------------------------------------+---------------------------
          Reporter:  valeriia.kalienkova@…  |      Owner:  Tristan Croll
              Type:  defect                 |     Status:  closed
          Priority:  normal                 |  Milestone:
         Component:  Third Party            |    Version:
        Resolution:  fixed                  |   Keywords:
        Blocked By:                         |   Blocking:
Notify when closed:                         |   Platform:  all
           Project:  ChimeraX               |
--------------------------------------------+---------------------------
Changes (by Tristan Croll):

 * resolution:   => fixed
 * status:  assigned => closed

Comment:

 I take it this is working for you now? I'm afraid I was a bit slack and
 didn't get the corrected template into the ISOLDE 1.6 release, but it's
 committed now.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8814#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker