![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#3586 closed enhancement (fixed)
Automatic log compacting
| Reported by: | Tristan Croll | Owned by: | pett |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Logging | Version: | |
| Keywords: | Cc: | Greg Couch, Tom Goddard | |
| 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
If it's feasible to do so, it might make the log quite a bit more compact/readable if it were to collate repeated identical commands into (e.g.) "isolde stepto (repeated 2000 times)"
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
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: 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
> 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: 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, 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
> clipper set contourSensitivity 0.25
> cofr centerOfView
> clipper spotlight radius 13.00
> clipper spotlight radius 14.00
> clipper spotlight radius 15.00
> clipper spotlight radius 16.00
> clipper spotlight radius 17.00
> select up
121741 atoms, 131332 bonds, 1 model selected
> select down
1852 atoms, 1129 bonds, 1 model selected
> close #1
Deleting atomic symmetry model...
> open 6zm7
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
> addh metalDist 1
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
23214 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
168870 hydrogens added
> open 11288 format ccp4 fromDatabase emdb
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
> select #1
394411 atoms, 410580 bonds, 5864 pseudobonds, 15 models selected
> select clear
> clipper set contourSensitivity 0.25
> select up
120529 atoms, 129986 bonds, 1 model selected
> select down
690 atoms, 669 bonds, 1 model selected
> delete sel
> hide HC
> select /CA
5546 atoms, 5592 bonds, 1 pseudobond, 2 models selected
> isolde restrain distances sel
> select clear
> select clear
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: H, OP1
> 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: 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, 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: H, OP1
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
Deleted the following atoms from the residue: OP1
> color sel bychain
> color sel byhetero
> select up
41 atoms, 42 bonds, 1 model selected
> select up
51 atoms, 52 bonds, 1 model selected
> select up
61 atoms, 62 bonds, 1 model selected
> select up
55526 atoms, 59874 bonds, 1 model selected
> select down
71 atoms, 62 bonds, 1 model selected
> select up
81 atoms, 82 bonds, 1 model selected
> select up
91 atoms, 92 bonds, 1 model selected
> select up
101 atoms, 102 bonds, 1 model selected
> delete sel
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
> delete sel
> select up
20 atoms, 19 bonds, 1 model selected
> select up
30 atoms, 29 bonds, 1 model selected
> select up
40 atoms, 39 bonds, 1 model selected
> select up
50 atoms, 49 bonds, 1 model selected
> select up
60 atoms, 59 bonds, 1 model selected
> select up
70 atoms, 69 bonds, 1 model selected
> select up
80 atoms, 79 bonds, 1 model selected
> select up
90 atoms, 89 bonds, 1 model selected
> delete sel
> color sel bychain
> color sel byhetero
> select /Lz
3603 atoms, 3631 bonds, 1 model selected
> isolde restrain distances sel
> select clear
> clipper spotlight radius 18.00
> clipper spotlight radius 19.00
> isolde stepto interpolateFrames 2
> isolde stepto interpolateFrames 2
> isolde stepto interpolateFrames 2
> isolde stepto interpolateFrames 2
> isolde stepto interpolateFrames 2
> ~hbonds
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde replace residue sel CA
> isolde start
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute
cmd.run(cmd_text)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/atomic/building/cmd.py", line 31, in replace_residue
match_by='element')
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/atomic/template_utils.py", line 198, in
fix_residue_from_template
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/atomic/template_utils.py", line 153, in
find_maximal_isomorphous_fragment
rg = residue_graph(residue, label=match_by)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/atomic/template_utils.py", line 99, in residue_graph
return make_graph_from_residue(residue, label=label)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue
return Graph(labels, edges)
RuntimeError: edges should be a n x 2 array of unsigned ints!
RuntimeError: edges should be a n x 2 array of unsigned ints!
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue
return Graph(labels, edges)
See log for complete Python traceback.
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto viewDistance 12
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> ui tool show Shell
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select clear
> select clear
> select clear
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> select clear
> delete sel
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> save /home/tic20/Desktop/rna_weird_h.jpg
> ui mousemode right label
> label #1.2/L5:243
> select clear
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde add ligand MG
> color sel bychain
> color sel byhetero
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute
cmd.run(cmd_text)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/atomic/building/place_ligand.py", line 160, in
place_ligand
fix_residue_to_match_md_template(session, r, ff._templates[md_template_name],
cif_template=tmpl)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/atomic/template_utils.py", line 324, in
fix_residue_to_match_md_template
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/atomic/template_utils.py", line 198, in
fix_residue_from_template
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/atomic/template_utils.py", line 153, in
find_maximal_isomorphous_fragment
rg = residue_graph(residue, label=match_by)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/atomic/template_utils.py", line 99, in residue_graph
return make_graph_from_residue(residue, label=label)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue
return Graph(labels, edges)
RuntimeError: edges should be a n x 2 array of unsigned ints!
RuntimeError: edges should be a n x 2 array of unsigned ints!
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue
return Graph(labels, edges)
See log for complete Python traceback.
> select clear
> select clear
> select clear
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> delete sel
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select ~CF
Expected an objects specifier or a keyword
> select /CF
452 atoms, 457 bonds, 1 model selected
> view sel
> isolde stepto
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
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 7.9G 44G 185M 9.8G 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 (5)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Logging |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Automatic log compacting |
| Type: | defect → enhancement |
comment:2 by , 5 years ago
follow-up: 3 comment:3 by , 5 years ago
No, not a mouse drag. Each command slides the view forward (or backward, depending on settings) by one residue along the chain.
comment:4 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Some simple-minded compaction will be in tomorrow's daily build (i.e. it won't be in 1.2). "Simple-minded" means that it only compacts repeated commands that had no output, which works for "isolde stepto" at least.
Would have been a lot trickier to compact commands that produce output, since the logging of the command text and command output occur in separate log() calls.
comment:5 by , 5 years ago
...and would only want to compact if the output was identical, which hopefully isn't too frequent.
Note:
See TracTickets
for help on using tickets.
While collation might be helpful are these "isolde stepto" commands the result of a mouse drag? If so we usually handle mouse drags by only logging an equivalent command on mouse release. Commands during a drag not only fill up the log but also can reduce performance while the user does the drag.