ISOLDE: 5-bond carbon

[tmckeith@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Trying to set things up for Isolde simulation, but serines couldn't be corrected. 
Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having 5 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (SER). If this template is built into ISOLDE, please report this using Help/Report a bug

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 3.pdb"

VAV1 working 3.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for VAV1 working 3.pdb #1  
---  
Chain | Description  
A B C D E F G I | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  
Non-standard residues in VAV1 working 3.pdb #1  
---  
ACE — (ACE)  
ADP — (ADP)  
ATP — (ATP)  
PTR — (PTR)  
  

> set bgColor white

> open /Users/tmckeithan/Downloads/Chimera/PDB/6ZNL.pdb

6ZNL.pdb title:  
Cryo-em structure of the dynactin complex [more info...]  
  
Chain information for 6ZNL.pdb #2  
---  
Chain | Description | UniProt  
A B C D E F G I | ARP1 actin related protein 1 homolog A | F2Z5G5_PIG 1-376  
H | β-actin | ACTB_PIG 1-375  
J | ARP11 | I3LHK5_PIG 1-417  
K | capping protein (actin filament) muscle Z-line, α 1 | A0PFK5_PIG 1-286  
L | F-actin capping protein β subunit | A9XFX6_PIG 1-272  
M N m n | dynactin subunit 2 |  
O o | dynactin subunit 3 isoform 1 | F1SEC0_PIG 1-186  
U | dynactin 6 | D0G6S1_PIG 1-190  
V | dynactin subunit 5 |  
Y | dynactin subunit 4 |  
Z z | dynactin subunit 1 |  
  
Non-standard residues in 6ZNL.pdb #2  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
ZN — zinc ion  
  

> select add #2

52864 atoms, 53884 bonds, 24 pseudobonds, 7014 residues, 3 models selected  

> select #2/M

2238 atoms, 2259 bonds, 4 pseudobonds, 340 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> ui tool show "Show Sequence Viewer"

> close #2

> open /Users/tmckeithan/Downloads/Chimera/PDB/6ZNL.pdb

6ZNL.pdb title:  
Cryo-em structure of the dynactin complex [more info...]  
  
Chain information for 6ZNL.pdb #2  
---  
Chain | Description | UniProt  
A B C D E F G I | ARP1 actin related protein 1 homolog A | F2Z5G5_PIG 1-376  
H | β-actin | ACTB_PIG 1-375  
J | ARP11 | I3LHK5_PIG 1-417  
K | capping protein (actin filament) muscle Z-line, α 1 | A0PFK5_PIG 1-286  
L | F-actin capping protein β subunit | A9XFX6_PIG 1-272  
M N m n | dynactin subunit 2 |  
O o | dynactin subunit 3 isoform 1 | F1SEC0_PIG 1-186  
U | dynactin 6 | D0G6S1_PIG 1-190  
V | dynactin subunit 5 |  
Y | dynactin subunit 4 |  
Z z | dynactin subunit 1 |  
  
Non-standard residues in 6ZNL.pdb #2  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
ZN — zinc ion  
  

> select add #2

52864 atoms, 53884 bonds, 24 pseudobonds, 7014 residues, 3 models selected  

> select subtract #2/M

50626 atoms, 51625 bonds, 20 pseudobonds, 6674 residues, 3 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> ui tool show "Show Sequence Viewer"

[Repeated 1 time(s)]

> sequence chain #2/M

Alignment identifier is 2/M  

> select clear

> select #2/M:102-403

1653 atoms, 1664 bonds, 2 pseudobonds, 265 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select clear

> select #2/M

585 atoms, 595 bonds, 1 pseudobond, 75 residues, 2 models selected  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> combine #1,2 close true name VAV

> isolde sim start /K-M

> set selectionWidth 4

Done loading forcefield  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1 to IUPAC-IUB
standards.  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
Loading residue template for ADP from internal database  
Sim termination reason: None  
ISOLDE: stopped sim  
Loading residue template for ATP from internal database  
Fetching CCD MEN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MEN/MEN.cif  
Failed to add atoms ['HB3', 'HB2'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  
[Repeated 1 time(s)]Failed to add atoms ['HB3', 'HB2'] to atom C because this
will lead to having 5 atoms attached, which is more than its assigned geometry
can support. This is probably due to an error in the MD template (SER). If
this template is built into ISOLDE, please report this using Help/Report a bug  

> swapaa /M:56 tyr

Using Dunbrack library  
/M TYR 56: phi -54.0, psi -42.8 trans  
Applying TYR rotamer (chi angles: 179.2 103.5) to /M TYR 56  

> addh

Summary of feedback from adding hydrogens to VAV #1.2  
---  
warnings | Not adding hydrogens to /A GLU 232 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLU 235 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 237 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /I GLU 362 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /I GLU 364 CB because it is missing heavy-atom bond
partners  
11 messages similar to the above omitted  
Unknown hybridization for atom (CB) of residue type ARG; not adding hydrogens
to it  
notes | Termini for VAV (#1.2) chain A determined from SEQRES records  
Termini for VAV (#1.2) chain B determined from SEQRES records  
Termini for VAV (#1.2) chain C determined from SEQRES records  
Termini for VAV (#1.2) chain D determined from SEQRES records  
Termini for VAV (#1.2) chain E determined from SEQRES records  
8 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /K ACE 0, /L SER 2  
Chain-initial residues that are not actual N termini: /A ILE 7, /B ILE 7, /C
GLU 2, /D ILE 7, /E ILE 7, /F ILE 7, /G ILE 7, /H ALA 6, /I ILE 7, /J GLU 12,
/M ASP 3, /M LEU 37  
Chain-final residues that are actual C termini: /A PHE 376, /B PHE 376, /C PHE
376, /D PHE 376, /E PHE 376, /F PHE 376, /G PHE 376, /H PHE 375, /I PHE 376,
/K ASN 165  
Chain-final residues that are not actual C termini: /J LEU 390, /L ASN 172, /M
PRO 26, /M GLU 87  
3438 hydrogen bonds  
/J LEU 390 is not terminus, removing H atom from 'C'  
/L ASN 172 is not terminus, removing H atom from 'C'  
/M GLU 87 is not terminus, removing H atom from 'C'  
120 hydrogens added  
  

> isolde sim start /K-M

Sim termination reason: None  
ISOLDE: stopped sim  

MD template GLU for residue GLU M87 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.  

> swapaa /M:23 ser

Using Dunbrack library  
/M SER 23: phi -65.3, psi 129.7 trans  
Applying SER rotamer (chi angles: 175.9) to /M SER 23  

> swapaa /M:42 ser

Using Dunbrack library  
/M SER 42: phi -108.9, psi 152.6 trans  
Applying SER rotamer (chi angles: -63.5) to /M SER 42  

> swapaa /M:44 ser

Using Dunbrack library  
/M SER 44: phi -47.0, psi -59.0 trans  
Applying SER rotamer (chi angles: 179.3) to /M SER 44  

> swapaa /M:72 ser

Using Dunbrack library  
/M SER 72: phi -56.7, psi 164.4 trans  
Applying SER rotamer (chi angles: 68.1) to /M SER 72  

> swapaa /M:85 ser

Using Dunbrack library  
/M SER 85: phi -162.1, psi 167.5 trans  
Applying SER rotamer (chi angles: 68.0) to /M SER 85  

> isolde sim start /K-M

Sim termination reason: None  
ISOLDE: stopped sim  
Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  

> hide sel cartoons

> select

65883 atoms, 66653 bonds, 1 pseudobond, 4136 residues, 18 models selected  

> hide sel cartoons

Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  




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Locale: UTF-8
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[Eric Pettersen]

Reported by Tim McKeithan