Opened 5 years ago

Closed 5 years ago

#3584 closed defect (fixed)

Spurious H added to nucleic P

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Ran into this again, and decided it *is* annoying enough to warrant a proper bug report: AddH consistently adds a spurious hydrogen to the dangling P of 5' terminal RNA residues.

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/home/tic20/.cache/ChimeraX/1.0/installers/ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper~=0.13.0 in
/home/tic20/.local/share/ChimeraX/1.0/site-packages (from ChimeraX-
ISOLDE==1.0rc1) (0.13.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1)
(1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Arrays~=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1)
(1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-
Core~=1.0rc202005052344 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages
(from ChimeraX-ISOLDE==1.0rc1) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Geometry~=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-
Atomic>=1.0->ChimeraX-ISOLDE==1.0rc1) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Graphics~=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-
Atomic>=1.0->ChimeraX-ISOLDE==1.0rc1) (1.0)  
Installing collected packages: ChimeraX-ISOLDE  
Attempting uninstall: ChimeraX-ISOLDE  
Found existing installation: ChimeraX-ISOLDE 1.0rc1  
Uninstalling ChimeraX-ISOLDE-1.0rc1:  
Successfully uninstalled ChimeraX-ISOLDE-1.0rc1  
Successfully installed ChimeraX-ISOLDE-1.0rc1  
Lock 140020333521040 acquired on
/home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock  
Lock 140020333521040 released on
/home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock  
  

WARNING: You are using pip version 20.1; however, version 20.2 is available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

File /home/tic20/Downloads/2ycg-sf.cif does not appear to contain any valid
residue templates.  

File /home/tic20/Downloads/5lh0-sf.cif does not appear to contain any valid
residue templates.  

File /home/tic20/Downloads/5lh7-sf.cif does not appear to contain any valid
residue templates.  

File /home/tic20/Downloads/6i2m.cif does not appear to contain any valid
residue templates.  

File /home/tic20/Downloads/BAM.cif does not appear to contain any valid
residue templates.  

Loaded CIF templates for [CDL] from /home/tic20/Downloads/CDL.cif  
You will now be able to add these residues to your model with "isolde add
ligand {ID}". To be able to simulate them, you will need to provide matching
ffXML MD parameterisations.  

> open 6zm7

Summary of feedback from opening 6zm7 fetched from pdb  
---  
note | Fetching compressed mmCIF 6zm7 from
http://files.rcsb.org/download/6zm7.cif  
  
6zm7 title:  
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex [more
info...]  
  
Chain information for 6zm7 #1  
---  
Chain | Description  
CA | Proliferation-associated protein 2G4  
CC | tRNA  
CE | Coiled-coil domain-containing protein 124  
CF | Non-structural protein 1  
L5 | 28S ribosomal RNA  
L7 | 5S ribosomal RNA  
L8 | 5.8S ribosomal RNA  
LA | 60S ribosomal protein L8  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6  
LF | 60S ribosomal protein L7  
LG | 60S ribosomal protein L7a  
LH | 60S ribosomal protein L9  
LI | 60S ribosomal protein L10-like  
LJ | 60S ribosomal protein L11  
LL | 60S ribosomal protein L13  
LM | 60S ribosomal protein L14  
LN | 60S ribosomal protein L15  
LO | 60S ribosomal protein L13a  
LP | 60S ribosomal protein L17  
LQ | 60S ribosomal protein L18  
LR | 60S ribosomal protein L19  
LS | 60S ribosomal protein L18a  
LT | 60S ribosomal protein L21  
LU | 60S ribosomal protein L22  
LV | 60S ribosomal protein L23  
LW | 60S ribosomal protein L24  
LX | 60S ribosomal protein L23a  
LY | 60S ribosomal protein L26  
LZ | 60S ribosomal protein L27  
La | 60S ribosomal protein L27a  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L35a  
Lg | 60S ribosomal protein L34  
Lh | 60S ribosomal protein L35  
Li | 60S ribosomal protein L36  
Lj | 60S ribosomal protein L37  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | Ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41  
Lo | 60S ribosomal protein L36a  
Lp | 60S ribosomal protein L37a  
Lr | 60S ribosomal protein L28  
Ls | 60S acidic ribosomal protein P0  
Lt | 60S ribosomal protein L12  
Lz | 60S ribosomal protein L10a  
S2 | 18S ribosomal RNA  
SA | 40S ribosomal protein SA  
SB | 40S ribosomal protein S3a  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15a  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
Sf | Ubiquitin-40S ribosomal protein S27a  
Sg | Receptor of activated protein C kinase 1  
  
Non-standard residues in 6zm7 #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  
6zm7 title:  
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex [more
info...]  
  
Chain information for 6zm7  
---  
Chain | Description  
1.2/CA | Proliferation-associated protein 2G4  
1.2/CC | tRNA  
1.2/CE | Coiled-coil domain-containing protein 124  
1.2/CF | Non-structural protein 1  
1.2/L5 | 28S ribosomal RNA  
1.2/L7 | 5S ribosomal RNA  
1.2/L8 | 5.8S ribosomal RNA  
1.2/LA | 60S ribosomal protein L8  
1.2/LB | 60S ribosomal protein L3  
1.2/LC | 60S ribosomal protein L4  
1.2/LD | 60S ribosomal protein L5  
1.2/LE | 60S ribosomal protein L6  
1.2/LF | 60S ribosomal protein L7  
1.2/LG | 60S ribosomal protein L7a  
1.2/LH | 60S ribosomal protein L9  
1.2/LI | 60S ribosomal protein L10-like  
1.2/LJ | 60S ribosomal protein L11  
1.2/LL | 60S ribosomal protein L13  
1.2/LM | 60S ribosomal protein L14  
1.2/LN | 60S ribosomal protein L15  
1.2/LO | 60S ribosomal protein L13a  
1.2/LP | 60S ribosomal protein L17  
1.2/LQ | 60S ribosomal protein L18  
1.2/LR | 60S ribosomal protein L19  
1.2/LS | 60S ribosomal protein L18a  
1.2/LT | 60S ribosomal protein L21  
1.2/LU | 60S ribosomal protein L22  
1.2/LV | 60S ribosomal protein L23  
1.2/LW | 60S ribosomal protein L24  
1.2/LX | 60S ribosomal protein L23a  
1.2/LY | 60S ribosomal protein L26  
1.2/LZ | 60S ribosomal protein L27  
1.2/La | 60S ribosomal protein L27a  
1.2/Lb | 60S ribosomal protein L29  
1.2/Lc | 60S ribosomal protein L30  
1.2/Ld | 60S ribosomal protein L31  
1.2/Le | 60S ribosomal protein L32  
1.2/Lf | 60S ribosomal protein L35a  
1.2/Lg | 60S ribosomal protein L34  
1.2/Lh | 60S ribosomal protein L35  
1.2/Li | 60S ribosomal protein L36  
1.2/Lj | 60S ribosomal protein L37  
1.2/Lk | 60S ribosomal protein L38  
1.2/Ll | 60S ribosomal protein L39  
1.2/Lm | Ubiquitin-60S ribosomal protein L40  
1.2/Ln | 60S ribosomal protein L41  
1.2/Lo | 60S ribosomal protein L36a  
1.2/Lp | 60S ribosomal protein L37a  
1.2/Lr | 60S ribosomal protein L28  
1.2/Ls | 60S acidic ribosomal protein P0  
1.2/Lt | 60S ribosomal protein L12  
1.2/Lz | 60S ribosomal protein L10a  
1.2/S2 | 18S ribosomal RNA  
1.2/SA | 40S ribosomal protein SA  
1.2/SB | 40S ribosomal protein S3a  
1.2/SC | 40S ribosomal protein S2  
1.2/SD | 40S ribosomal protein S3  
1.2/SE | 40S ribosomal protein S4, X isoform  
1.2/SF | 40S ribosomal protein S5  
1.2/SG | 40S ribosomal protein S6  
1.2/SH | 40S ribosomal protein S7  
1.2/SI | 40S ribosomal protein S8  
1.2/SJ | 40S ribosomal protein S9  
1.2/SK | 40S ribosomal protein S10  
1.2/SL | 40S ribosomal protein S11  
1.2/SM | 40S ribosomal protein S12  
1.2/SN | 40S ribosomal protein S13  
1.2/SO | 40S ribosomal protein S14  
1.2/SP | 40S ribosomal protein S15  
1.2/SQ | 40S ribosomal protein S16  
1.2/SR | 40S ribosomal protein S17  
1.2/SS | 40S ribosomal protein S18  
1.2/ST | 40S ribosomal protein S19  
1.2/SU | 40S ribosomal protein S20  
1.2/SV | 40S ribosomal protein S21  
1.2/SW | 40S ribosomal protein S15a  
1.2/SX | 40S ribosomal protein S23  
1.2/SY | 40S ribosomal protein S24  
1.2/SZ | 40S ribosomal protein S25  
1.2/Sa | 40S ribosomal protein S26  
1.2/Sb | 40S ribosomal protein S27  
1.2/Sc | 40S ribosomal protein S28  
1.2/Sd | 40S ribosomal protein S29  
1.2/Se | 40S ribosomal protein S30  
1.2/Sf | Ubiquitin-40S ribosomal protein S27a  
1.2/Sg | Receptor of activated protein C kinase 1  
  
Non-standard residues in 6zm7 #1.2  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> view

> open 11288 fromDatabase emdb

Summary of feedback from opening 11288 fetched from emdb  
---  
note | Fetching compressed map 11288 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11288/map/emd_11288.map.gz  
  
Opened emd_11288.map, grid size 400,400,400, pixel 1.06, shown at level
0.0945, step 2, values float32  

> clipper associate #2 toModel #1

> addh

Summary of feedback from adding hydrogens to 6zm7 #1.2  
---  
warnings | Not adding hydrogens to /L5 C 3978 C4' because it is missing heavy-
atom bond partners  
Not adding hydrogens to /L5 C 3978 C3' because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L5 C 3979 C4' because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L5 C 3979 C3' because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L5 G 3980 C4' because it is missing heavy-atom bond
partners  
163 messages similar to the above omitted  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /Lz ARG 26 NE  
notes | Termini for 6zm7 (#1.2) chain L5 determined from SEQRES records  
Termini for 6zm7 (#1.2) chain L7 determined from SEQRES records  
Termini for 6zm7 (#1.2) chain L8 determined from SEQRES records  
Termini for 6zm7 (#1.2) chain LA determined from SEQRES records  
Termini for 6zm7 (#1.2) chain LB determined from SEQRES records  
81 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /L5 C 1, /L7 G 1, /L8 C 1,
/LC MET 1, /LH MET 1, /LW MET 1, /LY MET 1, /Ln MET 1, /Lz MET 1, /S2 U 1, /SD
MET 1, /SK MET 1, /SR MET 1, /SS MET 1, /SV MET 1, /SG MET 1, /CC U 1  
Chain-initial residues that are not actual N termini: /L5 G 642, /L5 C 903,
/L5 C 1047, /L5 G 1064, /L5 C 1167, /L5 G 1234, /L5 C 1714, /L5 C 2249, /L5 C
3584, /L5 C 4858, /LA GLY 2, /LB SER 2, /LD GLY 2, /LE PRO 42, /LE VAL 88, /LF
ASN 24, /LG LYS 26, /LI GLY 2, /LI GLY 114, /LJ GLN 3, /LL ALA 2, /LM VAL 2,
/LN GLY 2, /LO GLU 3, /LP VAL 2, /LQ GLY 2, /LR SER 2, /LS LYS 2, /LT THR 2,
/LU GLN 17, /LV SER 10, /LX LYS 37, /LZ GLY 2, /La PRO 2, /Lb ALA 2, /Lb VAL
89, /Lc LYS 9, /Ld ASN 18, /Le ALA 2, /Lf SER 2, /Lg VAL 2, /Lh ALA 2, /Li ALA
2, /Lj THR 2, /Lk PRO 2, /Ll SER 2, /Lm ILE 77, /Lo VAL 2, /Lp ALA 2, /Lr SER
2, /Ls ASP 5, /Lt PRO 7, /Lt ILE 104, /S2 U 287, /S2 C 730, /S2 C 746, /S2 C
785, /SA GLY 3, /SB VAL 21, /SE ALA 2, /SF ASP 16, /SF ARG 135, /SH SER 5, /SH
LYS 111, /SI GLY 2, /SL ALA 2, /SP ARG 10, /SQ SER 3, /ST PRO 2, /SU ALA 16,
/SX GLY 2, /Sa THR 2, /Sc ARG 5, /Sd GLY 2, /Sg THR 2, /SC GLU 59, /SJ PRO 2,
/SM VAL 11, /SN GLY 2, /SO GLU 12, /SW VAL 2, /SY ASN 2, /SZ ARG 41, /Sb PRO
2, /Se VAL 2, /Sf TYR 85, /CA GLN 7, /CA GLU 286, /CE ASN 9, /CE ASP 162, /CF
ASP 152  
Chain-final residues that are actual C termini: /LB ALA 403, /LE PHE 288, /LF
ASN 248, /LG GLY 266, /LI SER 214, /LJ LYS 178, /LL LYS 211, /LN ARG 204, /LO
VAL 203, /LQ ASN 188, /LS PHE 176, /LT ALA 160, /LV ALA 140, /LX ILE 156, /LZ
PHE 136, /La ALA 148, /Lf ILE 110, /Lh ALA 123, /Lk LYS 70, /Ll LEU 51, /Lm
LYS 128, /Lo PHE 106, /Lp GLN 92, /Lz TYR 217, /S2 A 1869, /SE GLY 263, /SF
ARG 204, /SQ ARG 146, /SR VAL 135, /SU ALA 119, /SV PHE 83, /Sd ASP 56, /SM
LYS 132, /SN ALA 151, /SO LEU 151, /SW PHE 130, /Sb HIS 84, /Se SER 59, /CC A
75, /CF GLY 180  
Chain-final residues that are not actual C termini: /L5 C 519, /L5 G 760, /L5
G 996, /L5 G 1051, /L5 U 1100, /L5 A 1222, /L5 C 1709, /L5 G 2113, /L5 G 2910,
/L5 G 4776, /L5 U 5069, /L7 U 120, /L8 U 156, /LA THR 249, /LC LYS 368, /LD
ALA 294, /LE ALA 76, /LH ALA 190, /LI MET 102, /LM PRO 140, /LP GLU 154, /LR
LEU 188, /LU ILE 117, /LW LYS 124, /LY LYS 134, /Lb VAL 76, /Lb LYS 122, /Lc
ARG 106, /Ld GLU 124, /Le LEU 129, /Lg LYS 115, /Li LYS 103, /Lj LYS 87, /Ln
SER 24, /Lr VAL 126, /Ls ASN 200, /Lt GLU 87, /Lt PRO 163, /S2 G 225, /S2 G
698, /S2 C 739, /S2 C 753, /SA THR 223, /SB GLU 234, /SD LYS 227, /SF GLY 129,
/SH LYS 107, /SH GLN 193, /SI GLY 207, /SK ARG 98, /SL GLN 154, /SP SER 138,
/SS THR 145, /ST LYS 144, /SX ARG 142, /Sa PRO 103, /Sc LEU 68, /Sg ILE 314,
/SC VAL 280, /SG LEU 237, /SJ GLY 186, /SY LYS 132, /SZ GLY 115, /Sf ASN 151,
/CA PHE 283, /CA ALA 362, /CE LEU 81, /CE MET 212  
Missing OXT added to C-terminal residue /LB ALA 403  
Missing OXT added to C-terminal residue /LJ LYS 178  
Missing OXT added to C-terminal residue /Lo PHE 106  
Missing OXT added to C-terminal residue /SQ ARG 146  
Missing OXT added to C-terminal residue /SR VAL 135  
2 messages similar to the above omitted  
23213 hydrogen bonds  
Adding 'H' to /LA GLY 2  
Adding 'H' to /LB SER 2  
Adding 'H' to /LD GLY 2  
Adding 'H' to /LE VAL 88  
Adding 'H' to /LF ASN 24  
64 messages similar to the above omitted  
/LA THR 249 is not terminus, removing H atom from 'C'  
/LC LYS 368 is not terminus, removing H atom from 'C'  
/LD ALA 294 is not terminus, removing H atom from 'C'  
/LE ALA 76 is not terminus, removing H atom from 'C'  
/LH ALA 190 is not terminus, removing H atom from 'C'  
46 messages similar to the above omitted  
168866 hydrogens added  
  

> set bgColor white

Deleted the following atoms from the residue: OP1, H  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: H, OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1, H  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1, H  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1, H  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: H, OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1, H  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1, H  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1, H  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1, H  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1, H  

> color sel bychain

> color sel byhetero

Deleted the following atoms from the residue: OP1, H  

> color sel bychain

> color sel byhetero

> select clear




OpenGL version: 3.3.0 NVIDIA 450.51.05
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        7.3G         46G        168M        9.3G         54G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Spurious H added to nucleic P

Both truly terminal, and "terminal" in a missing-structure gap. Examples in 6zm7:

true terminus:
/L7:1
/CC:1

missing-structure "terminus":
/L5:642
/S2:287

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed
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