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Opened 5 years ago
Closed 5 years ago
#3663 closed defect (fixed)
Typo in graphics/drawing.py
| Reported by: | Tristan Croll | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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: 1.1rc202008252015 (2020-08-25 20:15:37 UTC)
Description
Took me an embarrassingly long time to spot what was going wrong here. Simple typo at line 1990 of drawing.py:
{{{
- pm = self._posititions_mask
+ pm = self._positions_mask
}}}
Log:
UCSF ChimeraX version: 1.1rc202008252015 (2020-08-25)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Wed Aug 12 09:29:54 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Tue Aug 11 14:56:35 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Mon Aug 10 22:18:52 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Mon Aug 10 22:10:12 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Mon Aug 10 17:52:30 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Sun Aug 9 20:59:39 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open broken.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Sun Aug 9 12:29:04 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Sat Aug 8 22:34:24 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open hydroxyhis/working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Fri Aug 7 18:39:29 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /run/media/tic20/storage/structure_dump/covid-19/6zm7/working_LI_49_cys.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Thu Aug 6 22:30:28 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Sun Aug 2 20:18:10 2020UCSF 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
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> isolde stepto
> isolde stepto viewDistance 12
> isolde stepto
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> 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
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> save /home/tic20/Desktop/rna_weird_h.jpg
> ui mousemode right label
> label #1.2/L5:243
> select clear
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> 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
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> select ~CF
Expected an objects specifier or a keyword
> select /CF
452 atoms, 457 bonds, 1 model selected
> view sel
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[deleted large part of log to get within ticket-length limit]
> 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")
> select up
14 atoms, 14 bonds, 1 model selected
> select up
348 atoms, 354 bonds, 1 model selected
> select clear
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> 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
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select up
15 atoms, 14 bonds, 1 model selected
> select up
124 atoms, 124 bonds, 1 model selected
> 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 sel
> isolde stepto
> isolde stepto
> select up
24 atoms, 23 bonds, 1 model selected
> select up
124 atoms, 124 bonds, 1 model selected
> select up
141 atoms, 140 bonds, 1 model selected
> select up
268 atoms, 268 bonds, 1 model selected
> 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
> select up
19 atoms, 18 bonds, 1 model selected
> 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
> select up
7 atoms, 6 bonds, 1 model selected
> select up
664 atoms, 671 bonds, 1 model selected
> 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
> select up
19 atoms, 18 bonds, 1 model selected
> select up
270 atoms, 270 bonds, 1 model selected
> select /SM
1906 atoms, 1916 bonds, 1 model selected
> select clear
> select clear
> select clear
> isolde jumpto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> 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
> select clear
> 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
> select up
31 atoms, 29 bonds, 1 model selected
> select up
198 atoms, 198 bonds, 1 model selected
> select clear
> 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
> 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
> 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
> 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
> select clear
> isolde stepto
> save working.cxs
Taking snapshot of stepper: 6zm7
> save working.cxs
Taking snapshot of stepper: 6zm7
> isolde stepto
> isolde stepto
> select up
17 atoms, 16 bonds, 1 model selected
> select up
228 atoms, 228 bonds, 1 model selected
> select clear
> delete sel
> isolde stepto
> isolde stepto /SC
Multiple residues selected! Going to the first...
> isolde jumpto
> isolde jumpto
> isolde jumpto
> isolde jumpto
> isolde jumpto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select up
16 atoms, 15 bonds, 1 model selected
> select up
161 atoms, 161 bonds, 1 model selected
> 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
> 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 up
26 atoms, 24 bonds, 1 model selected
> select up
184 atoms, 183 bonds, 1 model selected
> 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
> select clear
> 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
> select clear
> select clear
> 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
> 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
> open 4ybb
Summary of feedback from opening 4ybb fetched from pdb
---
notes | Fetching CCD PG4 from http://ligand-
expo.rcsb.org/reports/P/PG4/PG4.cif
Fetching CCD MPD from http://ligand-expo.rcsb.org/reports/M/MPD/MPD.cif
Fetching CCD PUT from http://ligand-expo.rcsb.org/reports/P/PUT/PUT.cif
Fetching CCD SPD from http://ligand-expo.rcsb.org/reports/S/SPD/SPD.cif
Fetching CCD 1PE from http://ligand-expo.rcsb.org/reports/1/1PE/1PE.cif
Fetching CCD PGE from http://ligand-expo.rcsb.org/reports/P/PGE/PGE.cif
Fetching CCD ACY from http://ligand-expo.rcsb.org/reports/A/ACY/ACY.cif
Fetching CCD GUN from http://ligand-expo.rcsb.org/reports/G/GUN/GUN.cif
Fetching CCD TRS from http://ligand-expo.rcsb.org/reports/T/TRS/TRS.cif
Fetching CCD G7M from http://ligand-expo.rcsb.org/reports/G/G7M/G7M.cif
Fetching CCD 4OC from http://ligand-expo.rcsb.org/reports/4/4OC/4OC.cif
Fetching CCD D2T from http://ligand-expo.rcsb.org/reports/D/D2T/D2T.cif
Fetching CCD 1MG from http://ligand-expo.rcsb.org/reports/1/1MG/1MG.cif
Fetching CCD 3TD from http://ligand-expo.rcsb.org/reports/3/3TD/3TD.cif
Fetching CCD 2MA from http://ligand-expo.rcsb.org/reports/2/2MA/2MA.cif
Fetching CCD 4D4 from http://ligand-expo.rcsb.org/reports/4/4D4/4D4.cif
Fetching CCD H2U from http://ligand-expo.rcsb.org/reports/H/H2U/H2U.cif
Fetching CCD MEQ from http://ligand-expo.rcsb.org/reports/M/MEQ/MEQ.cif
4ybb title:
High-resolution structure of the Escherichia coli ribosome [more info...]
Chain information for 4ybb #2
---
Chain | Description
AA BA | 16S rRNA
AB BB | 30S ribosomal protein S2
AC BC | 30S ribosomal protein S3
AD BD | 30S ribosomal protein S4
AE BE | 30S ribosomal protein S5
AF BF | 30S ribosomal protein S6
AG BG | 30S ribosomal protein S7
AH BH | 30S ribosomal protein S8
AI BI | 30S ribosomal protein S9
AJ BJ | 30S ribosomal protein S10
AK BK | 30S ribosomal protein S11
AL BL | 30S ribosomal protein S12
AM BM | 30S ribosomal protein S13
AN BN | 30S ribosomal protein S14
AO BO | 30S ribosomal protein S15
AP BP | 30S ribosomal protein S16
AQ BQ | 30S ribosomal protein S17
AR BR | 30S ribosomal protein S18
AS BS | 30S ribosomal protein S19
AT BT | 30S ribosomal protein S20
AU BU | 30S ribosomal protein S21
C0 D0 | 50S ribosomal protein L30
C1 D1 | 50S ribosomal protein L32
C2 D2 | 50S ribosomal protein L33
C3 D3 | 50S ribosomal protein L34
C4 D4 | 50S ribosomal protein L35
C5 D5 | 50S ribosomal protein L36
CA | 23S rRNA
CB DB | 5S rRNA
CC DC | 50S ribosomal protein L2
CD DD | 50S ribosomal protein L3
CE DE | 50S ribosomal protein L4
CF DF | 50S ribosomal protein L5
CG DG | 50S ribosomal protein L6
CH DH | 50S ribosomal protein L9
CJ DJ | 50S ribosomal protein L11
CK DK | 50S ribosomal protein L13
CL DL | 50S ribosomal protein L14
CM DM | 50S ribosomal protein L15
CN DN | 50S ribosomal protein L16
CO DO | 50S ribosomal protein L17
CP DP | 50S ribosomal protein L18
CQ DQ | 50S ribosomal protein L19
CR DR | 50S ribosomal protein L20
CS DS | 50S ribosomal protein L21
CT DT | 50S ribosomal protein L22
CU DU | 50S ribosomal protein L23
CV DV | 50S ribosomal protein L24
CW DW | 50S ribosomal protein L25
CX DX | 50S ribosomal protein L27
CY DY | 50S ribosomal protein L28
CZ DZ | 50S ribosomal protein L29
DA | 23S rRNA
DI | 50S ribosomal protein L10
Non-standard residues in 4ybb #2
---
1PE — pentaethylene glycol (PEG400)
3TD —
(1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-
D-ribitol
4D4 — (2S,3R)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid
ACY — acetic acid
D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid
EDO — 1,2-ethanediol (ethylene glycol)
GUN — guanine
MG — magnesium ion
MPD — (4S)-2-methyl-2,4-pentanediol
PEG — di(hydroxyethyl)ether
PG4 — tetraethylene glycol
PGE — triethylene glycol
PUT — 1,4-diaminobutane (putrescine)
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
ZN — zinc ion
4ybb mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> matchmaker #2/AK to #1/SO
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6zm7, chain SO (#1.2) with 4ybb, chain AK (#2), sequence alignment
score = 224.4
RMSD between 87 pruned atom pairs is 0.977 angstroms; (across all 117 pairs:
3.661)
> hide #2&~/AK
> select #2
294856 atoms, 311232 bonds, 10729 pseudobonds, 4 models selected
> style sel stick
Changed 294856 atom styles
> select clear
> color #2 byhetero
> select clear
> close #2
> open 4cvn
Summary of feedback from opening 4cvn fetched from pdb
---
note | Fetching compressed mmCIF 4cvn from
http://files.rcsb.org/download/4cvn.cif
4cvn title:
Structure of the Fap7-Rps14 complex [more info...]
Chain information for 4cvn #2
---
Chain | Description
A B C D | putative adenylate kinase
E F G H | 30S ribosomal protein S11
Non-standard residues in 4cvn #2
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
4cvn mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
> matchmaker #2/E to #1/SO
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6zm7, chain SO (#1.2) with 4cvn, chain E (#2), sequence alignment
score = 463.1
RMSD between 96 pruned atom pairs is 0.824 angstroms; (across all 126 pairs:
7.008)
> select #2
9743 atoms, 9377 bonds, 29 pseudobonds, 3 models selected
> style sel stick
Changed 9743 atom styles
> close #2
> isolde stepto
> isolde stepto
> isolde stepto
> 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
> select up
17 atoms, 17 bonds, 1 model selected
> select up
45 atoms, 46 bonds, 1 model selected
> 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
> select up
17 atoms, 17 bonds, 1 model selected
> select up
70 atoms, 70 bonds, 1 model selected
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> 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
> isolde stepto
> 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
> 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
> 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
> select up
33 atoms, 31 bonds, 1 model selected
> select up
151 atoms, 150 bonds, 1 model selected
> 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
> select up
7 atoms, 6 bonds, 1 model selected
> select up
97 atoms, 98 bonds, 1 model selected
> 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
> select up
14 atoms, 13 bonds, 1 model selected
> select up
92 atoms, 92 bonds, 1 model selected
> 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
> 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
> 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 up
22 atoms, 21 bonds, 1 model selected
> select up
170 atoms, 171 bonds, 1 model selected
> select clear
> save working.cxs
Taking snapshot of stepper: 6zm7
> 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
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select up
24 atoms, 23 bonds, 1 model selected
> select up
61 atoms, 60 bonds, 1 model selected
> select clear
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> delete sel
> isolde stepto sel
> isolde stepto
> select up
19 atoms, 18 bonds, 1 model selected
> select up
191 atoms, 191 bonds, 1 model selected
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> 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
> select up
19 atoms, 18 bonds, 1 model selected
> select up
139 atoms, 140 bonds, 1 model selected
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select up
22 atoms, 21 bonds, 1 model selected
> select up
91 atoms, 90 bonds, 1 model selected
> 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
> select up
7 atoms, 6 bonds, 1 model selected
> select up
26 atoms, 25 bonds, 1 model selected
> 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 up
16 atoms, 15 bonds, 1 model selected
> select up
152 atoms, 152 bonds, 1 model selected
> 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
> select up
17 atoms, 16 bonds, 1 model selected
> select up
252 atoms, 254 bonds, 1 model selected
> 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
> select up
16 atoms, 15 bonds, 1 model selected
> select up
417 atoms, 418 bonds, 1 model selected
> select clear
> 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
> 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
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select up
22 atoms, 21 bonds, 1 model selected
> select up
254 atoms, 254 bonds, 1 model selected
> 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
> swapaa mousemode sel LYS
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select up
14 atoms, 13 bonds, 1 model selected
> select up
395 atoms, 398 bonds, 1 model selected
> 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
> delete sel
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> 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 jumpto
> isolde stepto
> select /CC
2399 atoms, 2583 bonds, 1 model selected
> 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
> select /CC
2399 atoms, 2583 bonds, 1 model selected
> 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
> select /CF
452 atoms, 457 bonds, 1 model selected
> isolde stepto
> save working.cxs
Taking snapshot of stepper: 6zm7
opened ChimeraX session
> view /SF:78
> select /SF:79@CA
1 atom, 1 model selected
> isolde start
> set selectionWidth 4
Done loading forcefield
> select clear
> select clear
> 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
> save working.cxs
Taking snapshot of stepper: 6zm7
opened ChimeraX session
> isolde start
> set selectionWidth 4
Done loading forcefield
> select /CE
2107 atoms, 2119 bonds, 1 pseudobond, 2 models selected
> 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
> select /CE:43-500
1580 atoms, 1589 bonds, 1 pseudobond, 2 models selected
> 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
> 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
> select /CF
452 atoms, 457 bonds, 1 model selected
> 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
> select /CE
2107 atoms, 2119 bonds, 1 pseudobond, 2 models selected
> select clear
> select clear
> select clear
> select clear
> 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
> clipper spotlight radius 18.00
> select ~/Lt
390945 atoms, 407068 bonds, 396 pseudobonds, 23 models selected
> select ~/Lt,Ls
387908 atoms, 404008 bonds, 396 pseudobonds, 23 models selected
> select clear
> select clear
> select clear
> ui mousemode right distance
> distance /S2:1271@OP2 /Sf:93@CA
Distance between /S2 C 1271 OP2 and /Sf HIS 93 CA: 9.395Å
> ~distance
> distance /Sf:94@NZ /S2:1507@P
Distance between /Sf LYS 94 NZ and /S2 G 1507 P: 5.472Å
> ~distance
> select clear
> save working.cxs
Taking snapshot of stepper: 6zm7
> select ~H
224627 atoms, 409203 bonds, 397 pseudobonds, 23 models selected
> save working_noh.cif #1 selectedOnly true
> select clear
> view /SO:137
> view /L5:42
> select clear
> view /L5:98
> select clear
> select clear
> view /L5:42
> select clear
> view /L5:134
> select clear
> select clear
> view /L5:135
> view /L5:170
> select clear
> view /L5:200
> select clear
> select clear
> view /L5:233
> select clear
> select clear
> view /L5:234
> select clear
> view /L5:265
> view /L5:278
> select clear
> view /L5:306
> select clear
> view /L5:315
> select clear
> view /L5:406
> select clear
> view /L5:408
> select clear
> select clear
> view /L5:409
> select clear
> select clear
> view /L5:411
> select clear
> view /L5:453
> select clear
> view /L5:468
> select clear
> select clear
> view /L5:667
> select clear
> save working.cxs
Taking snapshot of stepper: 6zm7
> select clear
> 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")
> select clear
> select up
53 atoms, 53 bonds, 1 model selected
> select up
120217 atoms, 129667 bonds, 1 model selected
> select down
53 atoms, 53 bonds, 1 model selected
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> save working.cxs
Taking snapshot of stepper: 6zm7
opened ChimeraX session
> isolde start
> set selectionWidth 4
Done loading forcefield
> select clear
> select clear
> save working.cxs
Taking snapshot of stepper: 6zm7
opened ChimeraX session
> select /ST:116@CA
1 atom, 1 residue, 1 model selected
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Drag select of 3 atoms, 2 bonds
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 529, in
_dispatch_mouse_event
lm.mouse_up(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 529, in
_dispatch_mouse_event
lm.mouse_up(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 529, in
_dispatch_mouse_event
lm.mouse_up(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 529, in
_dispatch_mouse_event
lm.mouse_up(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 529, in
_dispatch_mouse_event
lm.mouse_up(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 529, in
_dispatch_mouse_event
lm.mouse_up(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 210, in select_pick
session.logger.info('Drag select of %s' % _pick_description(pick))
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 226, in _pick_description
d = p.description()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
AttributeError: 'PickedInstance' object has no attribute '_posititions_mask'
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1990, in description
pm = self._posititions_mask
See log for complete Python traceback.
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 10G 29G 184M 22G 51G
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: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1rc202008252015
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.0.2
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-Phenix: 0.1
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.2
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.6
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 4.3.3
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Typo in graphics/drawing.py |
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed in 1.1 release branch and in develop.
Apparently no code was using this instance picking.