Add Hydrogens: Singular matrix

[petersx1@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
> open "C:\Users\User\Documents\Computational work\Mo\ligands\sdf files\mol2
> files\Avogadro optimized\cc_19_peptide.mol2" format mol2

Opened cc_19_peptide.mol2 containing 1 structure (191 atoms, 195 bonds)  

> select H

21 atoms, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Add Charges"

> addh

Summary of feedback from adding hydrogens to ***** #1  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\tool.py",
line 184, in add_h  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\hbond.py",
line 220, in add_hydrogens  
h_positions = bond_positions(atom._addh_coord, geom, bond_length,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 84, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 140, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 258, in angle_pos  
points.append(xform.inverse() * angle)  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\numpy\linalg\linalg.py",
line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\numpy\linalg\linalg.py",
line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\numpy\linalg\linalg.py",
line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4549
OpenGL renderer: Intel(R) HD Graphics 4600
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_ZA.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: XPS 8700
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 17,093,038,080
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
OSLanguage: en-US

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[pett]

Hi Xylia,

Thanks for reporting this problem. It typically occurs when there is something odd about the molecular structure, such as two atoms exactly on top of one another, or two exactly co-linear bonds attached to an atom. I would need access to your cc_19_peptide.mol2 file to offer any further insight.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[PetersX1@…]

Dear Eric,

I trust you are well.

Please find the attached peptide.

Kindly advise further.

Kind regards,
Xylia
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, March 11, 2024 8:49 PM
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Xylia Quintina Peters <PetersX1@ukzn.ac.za>
Subject: Re: [ChimeraX] #14742: Add Hydrogens: Singular matrix

#14742: Add Hydrogens: Singular matrix
----------------------------------------+----------------------
Reporter: petersx1@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+----------------------
Changes (by pett):

* status: accepted => feedback

Comment:

Hi Xylia,
Thanks for reporting this problem. It typically occurs when there
is something odd about the molecular structure, such as two atoms exactly
on top of one another, or two exactly co-linear bonds attached to an atom.
I would need access to your cc_19_peptide.mol2 file to offer any further
insight.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/14742#comment:2<https://url.za.m.mimecastprotect.com/s/jOY7CElQWDCq7qqpup-y0o?domain=rbvi.ucsf.edu>>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/<https://url.za.m.mimecastprotect.com/s/sx3RCGZKWGf8788AtQz5nf?domain=rbvi.ucsf.edu>>
ChimeraX Issue Tracker

UKZN email disclaimer:
The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University.

cc_19_peptide.mol2​

[PetersX1@…]

Added by email2trac

[pett]

Hi Xylia,

Thanks for supplying the structure. What is it supposed to represent? It has many carbon-carbon bond lengths of 0.825 (angstroms I hope), which is significantly shorter than even the standard carbon-carbon triple bond length (1.2 angstroms). You also have two atoms (C92 and C93) directly on top of one another. You would have to fix that latter problem with the structure before ChimeraX would be able to successfully add hydrogens.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[PetersX1@…]

Dear Eric,

I trust you are well.

This is a peptide a student is working on. He provided me with an SDF file that had the correct orientation, however; once optimized using Avogadro this changed. The structure I sent you was the one optimized. You can also see the 3D conformation. The SDF is flat. How else can we use Chimera to ensure the structure is well-optimized for adding hydrogen?

I've attached the sdf herein.

Please advise further.

Kind regards,
Xylia


________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, March 13, 2024 6:32 PM
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Xylia Quintina Peters <PetersX1@ukzn.ac.za>
Subject: Re: [ChimeraX] #14742: Add Hydrogens: Singular matrix

#14742: Add Hydrogens: Singular matrix
----------------------------------------+--------------------
Reporter: petersx1@… | Owner: pett
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: not a bug | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+--------------------
Changes (by pett):

* resolution: => not a bug
* status: feedback => closed

Comment:

Hi Xylia,
Thanks for supplying the structure. What is it supposed to
represent? It has many carbon-carbon bond lengths of 0.825 (angstroms I
hope), which is significantly shorter than even the standard carbon-carbon
triple bond length (1.2 angstroms). You also have two atoms (C92 and C93)
directly on top of one another. You would have to fix that latter problem
with the structure before ChimeraX would be able to successfully add
hydrogens.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/14742#comment:4<https://url.za.m.mimecastprotect.com/s/PX7FCO796QhOVoAghkbrLn?domain=rbvi.ucsf.edu>>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/<https://url.za.m.mimecastprotect.com/s/p4AhCP1JWRt6Yq42Hjqjst?domain=rbvi.ucsf.edu>>
ChimeraX Issue Tracker

UKZN email disclaimer:
The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University.

CC-19 peptide structure.sdf​

[PetersX1@…]

Added by email2trac

[pett]

Hi Xylia,

If you are using ChimeraX anyway, you might as use it to build the peptide as well. If I got the correct sequence from the visual inspection of your SDF structure, then in the current ChimeraX daily build the command "build start peptide CC-19 CRPRKWIKIKFRCKSVKFC -57,-47" would build the peptide as an alpha helix (phi/psi angles of -57/-47). You could also the "Add peptide" functionality of the Build Structure tool to do the same thing using a graphical user interface (which works in the 1.7 release you have installed, whereas a more complicated command would be needed in the 1.7 release versus the current daily build).
I hope this helps.

--Eric

[PetersX1@…]

Dear Eric,

I hope you are well.

Will try this. Thank you for your help.

Kind regards,
Xylia
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, March 15, 2024 3:43 AM
To: Xylia Quintina Peters <PetersX1@ukzn.ac.za>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #14742: Add Hydrogens: Singular matrix

#14742: Add Hydrogens: Singular matrix
----------------------------------------+--------------------
Reporter: petersx1@… | Owner: pett
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: not a bug | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+--------------------
Comment (by pett):

Hi Xylia,
If you are using ChimeraX anyway, you might as use it to build the
peptide as well. If I got the correct sequence from the visual inspection
of your SDF structure, then in the current ChimeraX daily build the
command "build start peptide CC-19 CRPRKWIKIKFRCKSVKFC -57,-47" would
build the peptide as an alpha helix (phi/psi angles of -57/-47). You
could also the "Add peptide" functionality of the Build Structure tool to
do the same thing using a graphical user interface (which works in the 1.7
release you have installed, whereas a more complicated command would be
needed in the 1.7 release versus the current daily build).
I hope this helps.

--Eric
--
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