Rebuild residue to template: template problem

[leofrancalima@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-47-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Hi Tristan,

I am the Leonardo that have has sent to you the e-mail about the use of the moderna08 force field on ISOLDE.

I've followed the protocoll you suggest on the ISOLD shell, uncommenting the line related to the moderna08 force field on the python script and reseting the forcefields on the ISOLDE main command line.

When I start an ISOLDE simulation with my system containing a 6TA RNA modification (although it is called "T6A" on my PDB, the software give me the option to parameterize it using the topology from MODRNA_6TA (in fact, the right topology), with a match score of 0.979, but returning "Not Found" on the CCD template and nothing on the "Description" field.

When I type on "Rebuild residue to template" anyway, ChimeraX give me the following reply:

"Failed to add atoms ['H22'] to atom C14 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 (MODRNA_6TA). If this template is built into ISOLDE, please report this using Help/Report a bug".

What could I try to fix it?

Thank you in advance,

Leonardo


Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 9-After-R55-chiAngle-updated-close-original-noHydrogens-coot-1.pdb

Summary of feedback from opening 9-After-R55-chiAngle-updated-close-original-
noHydrogens-coot-1.pdb  
---  
warnings | Duplicate atom serial number found: 1584  
Duplicate atom serial number found: 1585  
Duplicate atom serial number found: 1586  
Duplicate atom serial number found: 1587  
Duplicate atom serial number found: 1588  
42 messages similar to the above omitted  
  
Chain information for 9-After-R55-chiAngle-updated-close-original-noHydrogens-
coot-1.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
A | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
n | No description available  
  

> hide

> ribbon

> set bgColor white

> open /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/No-modification/Post-Phenix/After-Correction-
> QuadrisulfideBond-in-Chain-e/After-coot-R55-chiAngles-updating/with-all-the-
> nucle-modifications/NOTm6A-Postprocessresamp.mrc

Opened NOTm6A-Postprocessresamp.mrc as #2, grid size 384,384,384, pixel 1.1,
shown at level 0.0103, step 2, values float32  

> clipper associate #2 toModel #1

Opened NOTm6A-Postprocessresamp.mrc as #1.1.1.1, grid size 384,384,384, pixel
1.1, shown at level 0.0267, step 1, values float32  
Chain information for 9-After-R55-chiAngle-updated-close-original-noHydrogens-
coot-1.pdb  
---  
Chain | Description  
1.2/1 | No description available  
1.2/2 | No description available  
1.2/3 | No description available  
1.2/A | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
1.2/J | No description available  
1.2/K | No description available  
1.2/L | No description available  
1.2/M | No description available  
1.2/N | No description available  
1.2/O | No description available  
1.2/P | No description available  
1.2/Q | No description available  
1.2/R | No description available  
1.2/S | No description available  
1.2/T | No description available  
1.2/U | No description available  
1.2/V | No description available  
1.2/W | No description available  
1.2/X | No description available  
1.2/Y | No description available  
1.2/Z | No description available  
1.2/a | No description available  
1.2/b | No description available  
1.2/c | No description available  
1.2/d | No description available  
1.2/e | No description available  
1.2/f | No description available  
1.2/g | No description available  
1.2/i | No description available  
1.2/j | No description available  
1.2/k | No description available  
1.2/l | No description available  
1.2/n | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> select clear

> addh

Summary of feedback from adding hydrogens to 9-After-R55-chiAngle-updated-
close-original-noHydrogens-coot-1.pdb #1.2  
---  
warnings | Not adding hydrogens to /1 A 2 C5' because it is missing heavy-atom
bond partners  
Not adding hydrogens to /3 A 47 P because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for 9-After-R55-chiAngle-updated-close-
original-noHydrogens-coot-1.pdb (#1.2) chain 1; guessing termini instead  
No usable SEQRES records for 9-After-R55-chiAngle-updated-close-original-
noHydrogens-coot-1.pdb (#1.2) chain 2; guessing termini instead  
No usable SEQRES records for 9-After-R55-chiAngle-updated-close-original-
noHydrogens-coot-1.pdb (#1.2) chain 3; guessing termini instead  
No usable SEQRES records for 9-After-R55-chiAngle-updated-close-original-
noHydrogens-coot-1.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for 9-After-R55-chiAngle-updated-close-original-
noHydrogens-coot-1.pdb (#1.2) chain C; guessing termini instead  
35 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A CYS 6, /C GLY 3, /D LYS
19, /E GLY 30, /F MET 1, /G MET 1, /H THR 29, /I MET 1, /J SER 5, /K GLY 2, /L
MET 1, /M MET 1, /N MET 1, /O GLY 9, /P GLY 2, /Q SER 16, /R VAL 4, /S PRO 6,
/T MET 1, /U PRO 6, /V VAL 4, /W ALA 16, /X MET 1, /Y VAL 2, /Z MET 1, /a ASP
3, /b THR 2, /c MET 1, /d ARG 5, /e GLN 4, /f LYS 82, /g THR 2, /i VAL 76, /j
GLY 8, /k LYS 4, /l MET 1, /n ARG 41  
Chain-initial residues that are not actual N termini: /I THR 171, /I ARG 178,
/Z TYR 27  
Chain-final residues that are actual C termini: /C GLU 209, /G GLY 263, /H ARG
219, /I LEU 237, /J LEU 194, /K GLY 207, /L GLY 188, /M ARG 98, /N PHE 158, /O
LYS 132, /P ALA 151, /Q LEU 151, /S ARG 146, /V LYS 144, /W ALA 119, /Y PHE
130, /c HIS 84, /f LYS 152, /g ILE 314, /i SER 133, /j ILE 115, /k ASP 598, /l
LYS 25  
Chain-final residues that are not actual C termini: /A VAL 271, /D GLY 233, /E
THR 255, /F LYS 227, /I PRO 169, /I ILE 176, /R PRO 143, /T MET 126, /U LYS
150, /X PHE 83, /Z ARG 142, /Z LYS 25, /a GLY 128, /b ARG 100, /d LEU 68, /e
ASP 56, /n GLY 115  
7575 hydrogen bonds  
Adding 'H' to /I THR 171  
Adding 'H' to /I ARG 178  
Adding 'H' to /Z TYR 27  
/A VAL 271 is not terminus, removing H atom from 'C'  
/D GLY 233 is not terminus, removing H atom from 'C'  
/E THR 255 is not terminus, removing H atom from 'C'  
/F LYS 227 is not terminus, removing H atom from 'C'  
/R PRO 143 is not terminus, removing H atom from 'C'  
9 messages similar to the above omitted  
68893 hydrogens added  
  

> isolde reset forcefield

> view #1/2:1244¨

Expected an objects specifier or a view name or a keyword  

> view #1/2:1244

> select #1/2:1244

47 atoms, 48 bonds, 1 residue, 1 model selected  

> isolde sim start sel

ISOLDE: stopped sim  

> volume gaussian #1 bfactor 150

Opened NOTm6A-Postprocessresamp.mrc gaussian as #2, grid size 384,384,384,
pixel 1.1, shown at step 1, values float32  

> clipper associate #2 toModel #1

Opened NOTm6A-Postprocessresamp.mrc gaussian as #1.1.1.2, grid size
384,384,384, pixel 1.1, shown at step 1, values float32  
Failed to add atoms ['H22'] to atom C14 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 (MODRNA_6TA). If this template is
built into ISOLDE, please report this using Help/Report a bug  

MD template MODRNA_HNA for residue T6A 137 contains extra atoms that are not
in a coordinate template, and are not directly connected to existing atoms.
Since MD templates do not explicitly provide geometry,these atoms will not be
built.  

Failed to add atoms ['H22'] to atom C14 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 (MODRNA_HNA). If this template is
built into ISOLDE, please report this using Help/Report a bug  

MD template MODRNA_26A for residue T6A 137 contains extra atoms that are not
in a coordinate template, and are not directly connected to existing atoms.
Since MD templates do not explicitly provide geometry,these atoms will not be
built.  

Failed to add atoms ['H22'] to atom C14 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 (MODRNA_26A). If this template is
built into ISOLDE, please report this using Help/Report a bug  

> addh

Summary of feedback from adding hydrogens to 9-After-R55-chiAngle-updated-
close-original-noHydrogens-coot-1.pdb #1.2  
---  
warnings | Not adding hydrogens to /1 A 2 C5' because it is missing heavy-atom
bond partners  
Not adding hydrogens to /3 A 47 P because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for 9-After-R55-chiAngle-updated-close-
original-noHydrogens-coot-1.pdb (#1.2) chain 1; guessing termini instead  
No usable SEQRES records for 9-After-R55-chiAngle-updated-close-original-
noHydrogens-coot-1.pdb (#1.2) chain 2; guessing termini instead  
No usable SEQRES records for 9-After-R55-chiAngle-updated-close-original-
noHydrogens-coot-1.pdb (#1.2) chain 3; guessing termini instead  
No usable SEQRES records for 9-After-R55-chiAngle-updated-close-original-
noHydrogens-coot-1.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for 9-After-R55-chiAngle-updated-close-original-
noHydrogens-coot-1.pdb (#1.2) chain C; guessing termini instead  
35 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A CYS 6, /C GLY 3, /D LYS
19, /E GLY 30, /F MET 1, /G MET 1, /H THR 29, /I MET 1, /J SER 5, /K GLY 2, /L
MET 1, /M MET 1, /N MET 1, /O GLY 9, /P GLY 2, /Q SER 16, /R VAL 4, /S PRO 6,
/T MET 1, /U PRO 6, /V VAL 4, /W ALA 16, /X MET 1, /Y VAL 2, /Z MET 1, /a ASP
3, /b THR 2, /c MET 1, /d ARG 5, /e GLN 4, /f LYS 82, /g THR 2, /i VAL 76, /j
GLY 8, /k LYS 4, /l MET 1, /n ARG 41  
Chain-initial residues that are not actual N termini: /I THR 171, /I ARG 178,
/Z TYR 27  
Chain-final residues that are actual C termini: /C GLU 209, /G GLY 263, /H ARG
219, /I LEU 237, /J LEU 194, /K GLY 207, /L GLY 188, /M ARG 98, /N PHE 158, /O
LYS 132, /P ALA 151, /Q LEU 151, /S ARG 146, /V LYS 144, /W ALA 119, /Y PHE
130, /c HIS 84, /f LYS 152, /g ILE 314, /i SER 133, /j ILE 115, /k ASP 598, /l
LYS 25  
Chain-final residues that are not actual C termini: /A VAL 271, /D GLY 233, /E
THR 255, /F LYS 227, /I PRO 169, /I ILE 176, /R PRO 143, /T MET 126, /U LYS
150, /X PHE 83, /Z ARG 142, /Z LYS 25, /a GLY 128, /b ARG 100, /d LEU 68, /e
ASP 56, /n GLY 115  
6976 hydrogen bonds  
/A VAL 271 is not terminus, removing H atom from 'C'  
/D GLY 233 is not terminus, removing H atom from 'C'  
/E THR 255 is not terminus, removing H atom from 'C'  
/F LYS 227 is not terminus, removing H atom from 'C'  
/R PRO 143 is not terminus, removing H atom from 'C'  
9 messages similar to the above omitted  
1 hydrogens added  
  
Failed to add atoms ['H22'] to atom C14 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 (MODRNA_6TA). If this template is
built into ISOLDE, please report this using Help/Report a bug  
[Repeated 1 time(s)]




OpenGL version: 3.3.0 NVIDIA 470.141.03
OpenGL renderer: Quadro K4200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       9.6Gi       1.3Gi       198Mi        20Gi        21Gi
	Swap:          2.0Gi       264Mi       1.7Gi

Graphics:
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	Subsystem: NVIDIA Corporation GK104GL [Quadro K4200] [10de:1096]	
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    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Eric Pettersen]

Reported by Leonardo Lima

[Tristan Croll]

Immediate problem was fixed off-list (by renaming the residue to match the components dictionary entry). I do plan to revisit this code in the future, probably replacing the mechanism I'm using at the moment with the more fully-developed approach in RDKit... can't make any promises on timing right now, though.