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Opened 5 months ago
Last modified 5 months ago
#18018 assigned defect
Ambiguous prefix chooses arbitrary command
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | Version: | |
| Keywords: | Cc: | Eric Pettersen, Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
typing '~' in the commandline appears to abbreviate '~struts'. This is confusing, because '~' alone is ambiguous and not unique. For example the command '~clip' also starts with '~'. According to the documentation, abbreviations of commands should be unique. Is this a bug?
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Mon Jun 16 13:37:56 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Thu Oct 17 14:08:33 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Wed Oct 16 16:03:09 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Mon Sep 30 13:13:06 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Mon Sep 30 09:42:04 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Fri Sep 27 12:58:06 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_reference_session.cxs
> format session
Log from Wed Jun 26 10:40:37 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias cofron cofr centerofview showpivot 4,0.2
> alias cofroff cofr centerofview showpivot false
> alias paulsave save
> /Users/psauer/Documents/Processing/20240530_IVTT15/$1.png
> transparentbackground true format png supersample 3
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias paulclip cofr centerofview; style stick; surface cap false; clip near
> -2 far 6 position cofr; material transparentCastShadows false; lighting
> flat; graphics silhouettes false; transparency 70; volume step 1
> alias paulunclip view all; transparency 0; lighting soft
> alias paullight material transparentCastShadows true; lighting soft;
> transparency 70; style stick; show cartoon
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; #disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.1; transparency 70;
> cofr centerofview; clip near -2 far 6 position cofr; #color ##~num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_30 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 30; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette ^RdYlBu-5;
> lighting soft; view all; transparency 0
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias paulvis lighting soft; material transparentcastshadows false; style
> stick; color /* #2b8cbe; select :ANM; select up; select up; color sel pink;
> ~select; color :IDB* yellow; color byhetero; graphics silhouettes true;
> graphics silhouettes width 1; graphics silhouettes depthJump 0.1;
> transparency 60; hide H
> alias paullabel label /* residues color black height 0.8 bgcolor
> rgba(100%,100%,100%,0.6); ~label :HOH
> alias IDB view :IDB*; paulclip; volume step 1
> alias paulcolor color $*/m #e31a1c; color $*/s,t #a6cee3; color $*/L* &
> nucleic #1f78b4; color $*/L* & protein #a6cee3; color $*/S* & nucleic
> #ff7f00; color $*/S* & protein #fdbf6f; color $*/Pt* #33a02c; color $*/mR
> #b2df8a; color $*:ANM $*/X yellow; color $*/By,NC #fb9a99
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_30
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"
> buttonpanel Shortcuts add IDB command IDB
> buttonpanel Shortcuts add paulvis command paulvis
> buttonpanel Shortcuts add paullabel command paullabel
> buttonpanel Shortcuts add paulclip command paulclip
> buttonpanel Shortcuts add paullight command paullight
> buttonpanel Shortcuts add paulsave command paulsave
> buttonpanel Shortcuts add unclip command paulunclip
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/TI-
> Post_SSU_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/TI-
> Post_P-tRNA_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/TI_uL11_5LZZ.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/TI_uL10_5LZZ.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/TI_eEF2_7LS2.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/SSU_7LS2.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH2_SSU_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH2_PE-
> tRNA_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH2_A-
> tRNA_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH1_SSU_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH1_PE-
> tRNA_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/PreH1_A-
> tRNA_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/Nascent_chain.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/MDsnapshot_1403_Ala35Glu_Ala36_Glu_Ala37Glu.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/LSU_8GLP.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/LSU_7LS2.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/IDB_1403.cif
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/GTP_eEF2.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/Nascent_chain.cif
---
warnings | Unknown polymer entity '1' on line 146
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening
/Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/MDsnapshot_1403_Ala35Glu_Ala36_Glu_Ala37Glu.cif
---
warnings | Unknown polymer entity '1' on line 165
Unknown polymer entity '2' on line 878
Unknown polymer entity '3' on line 6200
Unknown polymer entity '4' on line 6334
Missing second atom in struct_conn "covale55"
Missing second atom in struct_conn "covale56"
Atom HH31 is not in the residue template for ACE /L:1B
Atom HH31 is not in the residue template for ACE /L:1Q
Atom H is not in the residue template for ALA /L:2
Atom CA is not in the residue template for NMA /L:3A
Atom CA is not in the residue template for NMA /L:3B
Atom HH31 is not in the residue template for ACE /L:4
Atom CA is not in the residue template for NMA /L:5A
Atom HH31 is not in the residue template for ACE /L:66
Atom CA is not in the residue template for NMA /L:73A
Atom HH31 is not in the residue template for ACE /L:74
Atom CA is not in the residue template for NMA /L:75A
Atom HH31 is not in the residue template for ACE /L:112A
Atom CA is not in the residue template for NMA /L:115A
Atom HH31 is not in the residue template for ACE /L:131
Atom CA is not in the residue template for NMA /L:133A
Atom HH31 is not in the residue template for ACE /L:134
Atom CA is not in the residue template for NMA /L:135A
Too many hydrogens missing from residue template(s) to warn about
Atom CA is not in the residue template for NMA /L:246A
Atom CA is not in the residue template for NMA /L:250A
Atom CA is not in the residue template for NMA /L:261A
Atom O3' is not in the residue template for ALA /y:39
Atom O is not in the residue template for SPC :27
Atom O is not in the residue template for SPC :28
Atom O is not in the residue template for SPC :30
Atom O is not in the residue template for SPC :32
Atom O is not in the residue template for SPC :31
195 messages similar to the above omitted
Atom O1 is not in the residue template for UNK :900
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening
/Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/IDB_1403.cif
---
warning | Unable to fetch template for '.': will connect using distance criteria
Chain information for TI-Post_SSU_8GLP.cif #1
---
Chain | Description
S2 | 18S rRNA
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 (uS12)
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 | FAU ubiquitin-like and ribosomal protein S30
Sf | Ubiquitin-40S ribosomal protein S27a
Sg | Receptor of activated protein C kinase 1
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for TI-Post_P-tRNA_8GLP.cif #2
---
Chain | Description
Pt | P-site tRNA
Chain information for TI_uL11_5LZZ.cif #3
---
Chain | Description
t | uL11
Chain information for TI_uL10_5LZZ.cif #4
---
Chain | Description
s | uL10
Chain information for TI_eEF2_7LS2.cif #5
---
Chain | Description
m | Elongation factor 2
Chain information for SSU_7LS2.cif #6
---
Chain | Description
A | Isoform 3 of Plasminogen activator inhibitor 1 RNA-binding protein
A3 | 40S ribosomal protein S18
B3 | 40S ribosomal protein S19
C3 | 40S ribosomal protein S20
D3 | 40S ribosomal protein S21
E3 | 40S ribosomal protein S23
F3 | 40S ribosomal protein S26
G3 | 40S ribosomal protein S28
H3 | 40S ribosomal protein S29
I3 | Receptor of activated protein C kinase 1
J3 | 40S ribosomal protein S2
K3 | 40S ribosomal protein S6
L3 | 40S ribosomal protein S9
M3 | 40S ribosomal protein S12
N3 | 40S ribosomal protein S13
O3 | 40S ribosomal protein S14
P3 | 40S ribosomal protein S15a
Q3 | 40S ribosomal protein S24
R3 | 40S ribosomal protein S25
S3 | 40S ribosomal protein S27-like
T3 | 40S ribosomal protein S30
U3 | Ubiquitin-40S ribosomal protein S27a
m2 | 18S rRNA
o2 | 40S ribosomal protein SA
p2 | 40S ribosomal protein S3a
q2 | 40S ribosomal protein S3
r2 | 40S ribosomal protein S4, X isoform
s2 | 40S ribosomal protein S5
t | 40S ribosomal protein S7
u | 40S ribosomal protein S8
v2 | 40S ribosomal protein S10
w2 | 40S ribosomal protein S11
x2 | 40S ribosomal protein S15
y2 | 40S ribosomal protein S16
z2 | 40S ribosomal protein S17
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for PreH2_SSU_8GLP.cif #7
---
Chain | Description
S2 | 18S rRNA
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 (uS12)
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 | FAU ubiquitin-like and ribosomal protein S30
Sf | Ubiquitin-40S ribosomal protein S27a
Sg | Receptor of activated protein C kinase 1
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for PreH2_PE-tRNA_8GLP.cif #8
---
Chain | Description
Pt | P-site tRNA
Chain information for PreH2_A-tRNA_8GLP.cif #9
---
Chain | Description
Pt | P-site tRNA
Chain information for PreH1_SSU_8GLP.cif #10
---
Chain | Description
S2 | 18S rRNA
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 (uS12)
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 | FAU ubiquitin-like and ribosomal protein S30
Sf | Ubiquitin-40S ribosomal protein S27a
Sg | Receptor of activated protein C kinase 1
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for PreH1_PE-tRNA_8GLP.cif #11
---
Chain | Description
Pt | P-site tRNA
Chain information for PreH1_A-tRNA_8GLP.cif #12
---
Chain | Description
Pt | P-site tRNA
Chain information for Nascent_chain.cif #13
---
Chain | Description
By | Nascent protein chain
Chain information for MDsnapshot_1403_Ala35Glu_Ala36_Glu_Ala37Glu.cif #14
---
Chain | Description
L | No description available
L | No description available
P | No description available
y | No description available
Chain information for LSU_8GLP.cif #15
---
Chain | Description
L5 | 28S rRNA
L7 | 5S rRNA
L8 | 5.8S rRNA
LA | 60S ribosomal protein L8 (uL2)
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
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 | 60S ribosomal protein L40 (eL40)
Ln | 60S ribosomal protein L41
Lo | 60S ribosomal protein L36a
Lp | 60S ribosomal protein L37a
Lr | 60S ribosomal protein L28
124 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for LSU_7LS2.cif #16
---
Chain | Description
A1 | 60S ribosomal protein L7
A2 | 28S rRNA
B1 | 60S ribosomal protein L7a
B2 | 5S rRNA
C1 | 60S ribosomal protein L9
C2 | 5.8S rRNA
D1 | 60S ribosomal protein L10-like
D2 | 60S ribosomal protein L8
E1 | 60S ribosomal protein L11
E2 | 60S ribosomal protein L3
F1 | 60S ribosomal protein L13
F2 | 60S ribosomal protein L4
G1 | 60S ribosomal protein L14
G2 | 60S ribosomal protein L5
H1 | 60S ribosomal protein L15
H2 | 60S ribosomal protein L6
I2 | 60S ribosomal protein L13a
J2 | 60S ribosomal protein L17
K2 | 60S ribosomal protein L18
L2 | 60S ribosomal protein L19
M2 | 60S ribosomal protein L18a
N2 | 60S ribosomal protein L21
O2 | 60S ribosomal protein L22
P2 | 60S ribosomal protein L23
R2 | 60S ribosomal protein L23a
S2 | 60S ribosomal protein L26
T2 | 60S ribosomal protein L27
U2 | 60S ribosomal protein L27a
V2 | 60S ribosomal protein L29
W2 | 60S ribosomal protein L30
X2 | 60S ribosomal protein L31
Y2 | 60S ribosomal protein L32
Z2 | 60S ribosomal protein L35a
a2 | 60S ribosomal protein L34
b2 | 60S ribosomal protein L35
c2 | 60S ribosomal protein L36
d2 | 60S ribosomal protein L37
e2 | 60S ribosomal protein L38
f2 | 60S ribosomal protein L39
g2 | Ubiquitin-60S ribosomal protein L40
h2 | 60S ribosomal protein L41
i2 | 60S ribosomal protein L36a
j2 | 60S ribosomal protein L37a
k2 | 60S ribosomal protein L28
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> paulcolor
> style stick
Changed 606762 atom styles
> lighting soft
> help H
No help found for 'H'
> help H
No help found for 'H'
> hide H
> show cartoons
> hide atoms
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> alias paulcolor
Aliased "paulcolor" to: color $*/m #e31a1c; color $*/s,t #a6cee3; color $*/L*
& nucleic #1f78b4; color $*/L* & protein #a6cee3; color $*/S* & nucleic
#ff7f00; color $*/S* & protein #fdbf6f; color $*/Pt* #33a02c; color $*/mR
#b2df8a; color $*:ANM $*/X yellow; color $*/By,NC #fb9a99
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!16 models
> show #!16 models
> hide #18 models
> show #18 models
> hide #17 models
> hide #18 models
> show #!15 models
> hide #!15 models
> show #!6 models
> show #!5 models
> hide #!5 models
> hide #!16 models
> show #!16 models
> color #16 & nucleic #1f78b4
> color #16 & protein #a6cee3
> color #6 & nucleic #ff7f00
> color #6 & protein #fdbf6f
> color #6A #b2df8a
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> paulcolor
> color #16 & nucleic #1f78b4
> color #16 & protein #a6cee3
> color #6 & nucleic #ff7f00
> color #6 & protein #fdbf6f
> color #6A #b2df8a
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #16 & nucleic #1f78b4
> color #16 & protein #a6cee3
> color #6 & nucleic #ff7f00
> color #6 & protein #fdbf6f
> color #6/A #b2df8a
> hide molecule
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #!16 models
> hide #!6 models
> show #!1 models
> show #!2 models
> show #!15 models
> show #13 models
> alias Post hide #1-18 model; show 1,2,13,15 model
> hide #!2 models
> hide #!1 models
> show #4 models
> show #!6 models
> show #!8 models
> show #!10 models
> hide #13 models
> show #18 models
> Post
> show 1,2,13,15 model
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> alias Post hide #1-18 model; show #1,2,13,15 model
> Post
> save
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_reference_session.cxs
——— End of log from Wed Jun 26 10:40:37 2024 ———
opened ChimeraX session
> oo
> open
> /Users/psauer/Documents/Processing/ChimeraX_startup_preferences_Paul_20240911.cxc
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias hh hide H
> name roi (/Pt:76-77 /NC:249-end /By:21-end /X /L5:4397,4398,4450,4451,4452,4531,4532,3905,3908,4449,3907,4399,4519,4548,5258,5294,5301,5303,5348,5374,5384,5208,5401,5394,5167) | (/Pt:76-77 /NC:249-end /By:21-end /X /L5:4397,4398,4450,4451,4452,4531,4532,3905,3908,4449,3907,4399,4519,4548,5258,5294,5301,5303,5348,5374,5384,5208,5401,5394,5167) :<2.5 & :HOH
> name miniroi (/Pt:76-77 /NC:249-end /By:21-end /X)
> name froi :3905,3907,3908,4397,4449,5167,5394,5258 :<2.5 & :HOH | (:3905,3907,3908,4397,4449,5167,5394,5258)
> name broi :4398,4399,4450,4451,4452,4519,4531,4532,4548,5401,5208,5374,5384,5348,5294,5301,5303 :<2.5 & :HOH | (:4398, 4399,4450,4451,4452,4519,4531,4532,4548,5401,5208,5374,5384,5348,5294,5301,5303)
> alias cofron cofr centerofview showpivot 4,0.2
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias paulclip cofr centerofview; style stick; surface cap false; clip near
> -2 far 8 position cofr; material transparentCastShadows false; lighting
> flat; graphics silhouettes false; transparency 60; volume step 1
> alias paulunclip ~clip; transparency 0; lighting soft
> alias paulambience lighting fillInt 0.2 ambientInt 1.2 intensity 0.2
> multishadow 256 shadows false
> alias paullight material transparentCastShadows true; lighting soft;
> transparency 70; style stick; show cartoon
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; #disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.1; transparency 70;
> cofr centerofview; clip near -2 far 6 position cofr; #color ##~num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_30 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 30; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette ^RdYlBu-5;
> lighting soft; view all; transparency 0
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias paulvis lighting fillInt 0.2 ambientInt 1.2 intensity 0.2 multishadow
> 256 shadows false; material transparentcastshadows false; style $1 stick;
> transparency $1 60; nucleotides $1 atom; hide $1 cartoon; show $1 atoms;
> hide H; paulcolor $1
> alias paullabel label $* residues color black height 0.8 bgcolor
> rgba(100%,100%,100%,0.6); ~label :HOH
> alias IDB view :IDB*; paulclip; volume step 1
> alias paulcolor color $*/m #e31a1c; color $*/s,t #a6cee3; color $*/L* &
> nucleic #1f78b4; color $*/L* & protein #a6cee3; color $*/S* & nucleic
> #ff7f00; color $*/S* & protein #fdbf6f; color $*/Pt* #33a02c; color $*/mR
> #b2df8a; color $*:ANM $*/X yellow; color $*/By,NC #fb9a99
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_30
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"
> buttonpanel Shortcuts add IDB command IDB
> buttonpanel Shortcuts add paulvis command "paulvis #*"
> buttonpanel Shortcuts add paullabel command paullabel
> buttonpanel Shortcuts add paulclip command paulclip
> buttonpanel Shortcuts add paullight command paullight
> buttonpanel Shortcuts add paulsave command paulsave
> buttonpanel Shortcuts add unclip command paulunclip
> buttonpanel Shortcuts add paulambience command paulambience
executed ChimeraX_startup_preferences_Paul_20240911.cxc
> view list
No named views.
> view name v1
> turn y 1 90
> turn -y 1 180
> view name v2
> ui tool show "Side View"
> show #17 models
> show #17 atoms
> hh
> view list
Named views: v1, v2
> view name v3
> view v1
> view v3
[Repeated 1 time(s)]
> view name v4
> paulclip
Changed 606762 atom styles
> surface cap false
No volumes specified
> show #13,17#!1-2,15 atoms
> hh
> open
> /Users/psauer/Documents/Processing/20240917_IDB-1597/IDB-1597_LSU_model_final.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20240917_IDB-1597/IDB-1597_LSU_model_final.cif
---
warnings | Atom HO5' is not in the residue template for C /L8:1
Atom H3 is not in the residue template for OMU /L8:14
Atom H1 is not in the residue template for PSU /L8:55
Atom H1 is not in the residue template for PSU /L8:69
Atom H21 is not in the residue template for OMG /L8:75
Atom HO5' is not in the residue template for C /L5:1
Atom H21 is not in the residue template for OMG /L5:1316
Atom H61 is not in the residue template for 1MA /L5:1322
Atom H41 is not in the residue template for OMC /L5:1340
Too many hydrogens missing from residue template(s) to warn about
Atom N4 is not in the residue template for IDB /X:900
Chain information for IDB-1597_LSU_model_final.cif #19
---
Chain | Description
L5 | 28S rRNA
L7 | 5S rRNA
L8 | 5.8S rRNA
LA | 60S ribosomal protein L8 (uL2)
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
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 | 60S ribosomal protein L40 (eL40)
Ln | 60S ribosomal protein L41
Lo | 60S ribosomal protein L36a
Lp | 60S ribosomal protein L37a
Lr | 60S ribosomal protein L28
> open
> /Users/psauer/Documents/Processing/20240917_IDB-1597/cryosparc_P13_J26_005_volume_map_sharp.mrc
Opened cryosparc_P13_J26_005_volume_map_sharp.mrc as #20, grid size
512,512,512, pixel 0.834, shown at level 0.107, step 1, values float32
> paulvis #19
Changed 256432 atom styles
> mmaker #19 to #15 bring #20
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 LSU_8GLP.cif, chain L5 (#15) with IDB-1597_LSU_model_final.cif,
chain L5 (#19), sequence alignment score = 29206
RMSD between 3546 pruned atom pairs is 0.539 angstroms; (across all 3546
pairs: 0.539)
> mmaker #19/L5 to #15/L5 bring #20
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 LSU_8GLP.cif, chain L5 (#15) with IDB-1597_LSU_model_final.cif,
chain L5 (#19), sequence alignment score = 18161.4
RMSD between 3546 pruned atom pairs is 0.539 angstroms; (across all 3546
pairs: 0.539)
> nucleotides #13,17#!1-2,15,19 atoms
> style nucleic & #13,17#!1-2,15,19 stick
Changed 242843 atom styles
> style nuc stick
Expected a keyword
> style nuc #* stick
Expected a keyword
> style #* nuc stick
Expected a keyword
> style nucleic
> style nucleic stick
Changed 447328 atom styles
> paulclip
Changed 863194 atom styles
> cofron
> hide #17 models
> hide #13 models
> hide #!15 models
> hide #!2 models
> hide #!1 models
> cofroff
> view list
Named views: v1, v2, v3, v4
> view name v5
> paulambience
[Repeated 1 time(s)]
> color :IDB byhetero
> volume #20 level 0.1392
> view v5
> volume #20 level 0.14
> surface dust #20 size 2
> surface dust #20 size 1
> view v5
> view name v5
> set bgColor white
> graphics silhouettes true
> graphics silhouettes true width 1 depthJump 0.1
> paullabel
Label command requires an atom specifier to create labels.
> paullabel #19
Too many labels (11017), label texture size (4096,26460) exceeded maximum
OpenGL texture size (16384), some labels will be blank.
> alias paulsave
Aliased "paulsave" to: save
/Users/psauer/Documents/Processing/20240530_IVTT15/$1.png
transparentbackground true format png supersample 3
> centerofview showpivot false; surface cap t; wait 1; save
> /Users/psauer/Documents/Figures/Cartoons_and_images/$1.png
> transparentbackground true format png supersample 3; wait 1 ; surface cap f;
> wait 1
Expected fewer arguments
> alias paulsave cofr centerofview showpivot false; surface cap t; wait 1;
> save /Users/psauer/Documents/Figures/Cartoons_and_images/$1.png
> transparentbackground true format png supersample 3; wait 1 ; surface cap f;
> wait 1
> paulsave test
> surface cap true
> save /Users/psauer/Documents/Figures/Cartoons_and_images/test.png
> transparentBackground true format png supersample 3
> surface cap false
> ~label
> view v1
> hide atoms
> transparency 0
> lighting soft
> view 2
Expected an objects specifier or a view name or a keyword
> view v2
> view v4
> view v3
> view v4
> view v5
> close #19-20
> show #!15 models
> show #!1 models
> view v1
> graphics silhouettes false
> save
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_reference_session.cxs
——— End of log from Fri Sep 27 12:58:06 2024 ———
opened ChimeraX session
> ui tool show "Change Chain IDs"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #8
1645 atoms, 1837 bonds, 74 pseudobonds, 77 residues, 2 models selected
> show #!8 models
> show #!11 models
> select add #11
3290 atoms, 3674 bonds, 148 pseudobonds, 154 residues, 4 models selected
> ui tool show "Change Chain IDs"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> changechains sel Pt Et
Chain IDs of 154 residues changed
> changechains sel Pt Et
No residues specified have any of the 'from' chain IDs
> select clear
> hide #!8 models
> hide #!11 models
> view v1
> save
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_reference_session.cxs
——— End of log from Mon Sep 30 09:42:04 2024 ———
opened ChimeraX session
> view v5
> show #19 & roi atoms
> hh
> hide cartoons
> show #15 & roi atoms
> hh
> hide cartoons
> ~clip
> show #17 models
> show #17 atoms
> hh
> cofron
> hide froi atoms
> cofroff
> paulambience
> view list
Named views: v1, v2, v3, v4, v5
> view name v6
> ui tool show "Side View"
> view v6
> lighting depthCueStart 0.7
> lighting depthCueStart 0.8
> hide pbonds
> view name v6
> turn y 0 180
> turn y 180 180
> turn y 180
> hide broi atoms
> show froi atoms
> hh
> hide pbonds
> view v6
> hide froi atoms
> show broi atoms
> hh
> hide pbonds
> view v6
> show broi atoms
> show roi atoms
> hh
> hide broi atoms
> show roi atoms
> hh
> view v6
> select froi atoms
Expected a keyword
> select froi
388 atoms, 397 bonds, 20 pseudobonds, 36 residues, 6 models selected
> label
> select ~sel & ##selected
286497 atoms, 299766 bonds, 10464 pseudobonds, 29588 residues, 10 models
selected
> label roi atoms
> label roi residues
> ~label
> label roi residues
> select clear
> ~clip
> view v6
> select froi
388 atoms, 397 bonds, 20 pseudobonds, 36 residues, 6 models selected
> hide broi atoms
> view list
Named views: v1, v2, v3, v4, v5, v6
> view camera
Expected an objects specifier or a view name or a keyword
> view matrix
view matrix camera
0.75572,-0.041816,-0.65356,-77.536,0.65467,0.02214,0.75559,535.2,-0.017126,-0.99888,0.044107,205.22
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#7.3,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,1,0,0,0,0,1,0,0,0,0,1,0,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#12.2,1,0,0,0,0,1,0,0,0,0,1,0,#13,1,0,0,0,0,1,0,0,0,0,1,0,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,1,0,0,0,0,1,0,0,0,0,1,0,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#14.2,1,0,0,0,0,1,0,0,0,0,1,0,#15,1,0,0,0,0,1,0,0,0,0,1,0,#15.1,1,0,0,0,0,1,0,0,0,0,1,0,#15.2,1,0,0,0,0,1,0,0,0,0,1,0,#15.3,1,0,0,0,0,1,0,0,0,0,1,0,#15.4,1,0,0,0,0,1,0,0,0,0,1,0,#16,1,0,0,0,0,1,0,0,0,0,1,0,#16.1,1,0,0,0,0,1,0,0,0,0,1,0,#16.2,1,0,0,0,0,1,0,0,0,0,1,0,#17,1,0,0,0,0,1,0,0,0,0,1,0,#17.1,1,0,0,0,0,1,0,0,0,0,1,0,#18,1,0,0,0,0,1,0,0,0,0,1,0
> view list
Named views: v1, v2, v3, v4, v5, v6
> view name v7
> view v1
> select add #14
7309 atoms, 7315 bonds, 117 pseudobonds, 620 residues, 7 models selected
> select add #15
150751 atoms, 153121 bonds, 6726 pseudobonds, 19285 residues, 9 models
selected
> select add #16
286885 atoms, 300163 bonds, 10484 pseudobonds, 29624 residues, 11 models
selected
> select subtract #14
279795 atoms, 293068 bonds, 10384 pseudobonds, 29032 residues, 8 models
selected
> select subtract #15
136223 atoms, 147140 bonds, 3758 pseudobonds, 10343 residues, 3 models
selected
> select subtract #16
Nothing selected
> hide #!1,15,17 atoms
> show #!1,15,17 cartoons
> save
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_reference_session.cxs
> view v6
> show #15 & broi atoms
> show #17 atoms
> hh
> hide cartoons
> ~label
> color #17#!1,15 byhetero
> hide #!15 models
> ui mousemode right distance
> distance #17/X:900@C17 #17/X:900@C8
Distance between IDB_1403.cif #17/X . 900 C17 and C8: 6.023Å
> view name
Missing or invalid "name" argument: Expected a text string
> close #19
> view list
Named views: v1, v2, v3, v4, v5, v6, v7
> view name v8
> view v1
> show cartoons
> show #!15 models
> save
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_reference_session.cxs
——— End of log from Mon Sep 30 13:13:06 2024 ———
opened ChimeraX session
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J62_004_volume_map.mrc
Opened cryosparc_P17_J62_004_volume_map.mrc as #19, grid size 512,512,512,
pixel 0.834, shown at level 0.196, step 1, values float32
> fitmap #1-18 inMap #19
Fit molecules TI-Post_SSU_8GLP.cif (#1), TI-Post_P-tRNA_8GLP.cif (#2),
TI_uL11_5LZZ.cif (#3), TI_uL10_5LZZ.cif (#4), TI_eEF2_7LS2.cif (#5),
SSU_7LS2.cif (#6), PreH2_SSU_8GLP.cif (#7), PreH2_PE-tRNA_8GLP.cif (#8),
PreH2_A-tRNA_8GLP.cif (#9), PreH1_SSU_8GLP.cif (#10), PreH1_PE-tRNA_8GLP.cif
(#11), PreH1_A-tRNA_8GLP.cif (#12), Nascent_chain.cif (#13),
MDsnapshot_1403_Ala35Glu_Ala36_Glu_Ala37Glu.cif (#14), LSU_8GLP.cif (#15),
LSU_7LS2.cif (#16), IDB_1403.cif (#17), GTP_eEF2.cif (#18) to map
cryosparc_P17_J62_004_volume_map.mrc (#19) using 606762 atoms
average map value = 0.1795, steps = 156
shifted from previous position = 11.1
rotated from previous position = 2.74 degrees
atoms outside contour = 350147, contour level = 0.19583
Position of TI-Post_SSU_8GLP.cif (#1) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of TI-Post_P-tRNA_8GLP.cif (#2) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of TI_uL11_5LZZ.cif (#3) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of TI_uL10_5LZZ.cif (#4) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of TI_eEF2_7LS2.cif (#5) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of SSU_7LS2.cif (#6) relative to cryosparc_P17_J62_004_volume_map.mrc
(#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of PreH2_SSU_8GLP.cif (#7) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of PreH2_PE-tRNA_8GLP.cif (#8) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of PreH2_A-tRNA_8GLP.cif (#9) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of PreH1_SSU_8GLP.cif (#10) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of PreH1_PE-tRNA_8GLP.cif (#11) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of PreH1_A-tRNA_8GLP.cif (#12) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of Nascent_chain.cif (#13) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of MDsnapshot_1403_Ala35Glu_Ala36_Glu_Ala37Glu.cif (#14) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of LSU_8GLP.cif (#15) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of LSU_7LS2.cif (#16) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of IDB_1403.cif (#17) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
Position of GTP_eEF2.cif (#18) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99898856 0.03987075 0.02078889 -18.22085852
-0.04020046 0.99906843 0.01569085 10.77404400
-0.02014392 -0.01651071 0.99966075 16.35549484
Axis -0.33712288 0.42853160 -0.83827730
Axis point 288.12495929 489.25709244 0.00000000
Rotation angle (degrees) 2.73745222
Shift along axis -2.95075331
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/PreH1_AtRNA_classic.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
PS2_IDB-1289/PreH1_AtRNA_classic.cif
---
warnings | Atom H3 is not in the residue template for 4SU /Pt:8
Atom H3 is not in the residue template for H2U /Pt:21
Atom H41 is not in the residue template for OMC /Pt:33
Atom H1 is not in the residue template for PSU /Pt:56
Chain information for PreH1_AtRNA_classic.cif #20
---
Chain | Description
Pt | P-site tRNA
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/PreH1_AtRNA_non-classic.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
PS2_IDB-1289/PreH1_AtRNA_non-classic.cif
---
warnings | Atom H3 is not in the residue template for 4SU /Pt:8
Atom H3 is not in the residue template for H2U /Pt:21
Atom H41 is not in the residue template for OMC /Pt:33
Atom H1 is not in the residue template for PSU /Pt:56
Chain information for PreH1_AtRNA_non-classic.cif #21
---
Chain | Description
Pt | P-site tRNA
> paulvis #*
Changed 611738 atom styles
> set bgColor black
> paulclip
Changed 611738 atom styles
> cofron
> color #21 #73fa79ff
> show #13 models
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J163_003_volume_map.mrc
Opened cryosparc_P17_J163_003_volume_map.mrc as #22, grid size 512,512,512,
pixel 0.834, shown at level 0.186, step 1, values float32
> paulclip
Changed 611738 atom styles
> hide #!19 models
> volume #22 level 0.08695
> volume #22 level 0.09517
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J164_003_volume_map.mrc
Opened cryosparc_P17_J164_003_volume_map.mrc as #23, grid size 512,512,512,
pixel 0.834, shown at level 0.186, step 1, values float32
> hide #!22 models
> paulclip
Changed 611738 atom styles
> volume #23 level 0.1185
> volume #23 level 0.1648
> volume #23 level 0.1185
> hide #!23 models
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J162_003_volume_map.mrc
Opened cryosparc_P17_J162_003_volume_map.mrc as #24, grid size 512,512,512,
pixel 0.834, shown at level 0.186, step 1, values float32
> paulclip
Changed 611738 atom styles
> volume #24 level 0.1108
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J161_002_volume_map.mrc
Opened cryosparc_P17_J161_002_volume_map.mrc as #25, grid size 512,512,512,
pixel 0.834, shown at level 0.184, step 1, values float32
> hide #!24 models
> paulclip
Changed 611738 atom styles
> volume #25 level 0.1134
> hide #!23 models
> show #!25 models
> volume #25 level 0.0779
> volume #25 level 0.1016
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> volume #22 level 0.07834
> volume #22 level 0.1069
> show #!23 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> volume #23 level 0.1692
> volume #23 level 0.2385
> hide #!23 models
> show #!22 models
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J132_001_volume_map.mrc
Opened cryosparc_P17_J132_001_volume_map.mrc as #26, grid size 512,512,512,
pixel 0.834, shown at level 0.181, step 1, values float32
> paulclip
Changed 611738 atom styles
> hide #!22 models
> volume #26 level 0.1247
> volume #26 level 0.09106
> show #!26 models
> hide #!26 models
> show #!25 models
> show #!22 models
> hide #!25 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!25 models
> hide #!25 models
> show #!26 models
> volume #26 level 0.1018
> save /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/1289_myc_session.cxs includeMaps true
——— End of log from Wed Oct 16 16:03:09 2024 ———
opened ChimeraX session
> volume #26 level 0.1232
> paulunclip
> show #!19 models
> hide #!20 models
> hide #!21 models
> hide #!26 models
> show #!2 models
> volume zone #19 nearAtoms #15 & roi range 10
> hide #!15 models
> volume zone #19 nearAtoms #15 & roi range 20
> volume zone #19 nearAtoms #15 & roi range 20 newMap true
Opened cryosparc_P17_J62_004_volume_map.mrc zone as #27, grid size
512,512,512, pixel 0.834, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/PTC_zone_P17_J62_004_volume_map.mrc models #27
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J117_005_volume_map.mrc
Opened cryosparc_P17_J117_005_volume_map.mrc as #28, grid size 512,512,512,
pixel 0.834, shown at level 0.0846, step 1, values float32
> hide #!27 models
> paulclip
Changed 611738 atom styles
> cofron
> show #!15 models
> volume #28 level 0.0758
> volume #28 level 0.06257
> volume #28 level 0.05111
> hide #!28 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> show #!28 models
> volume zone #19 nearAtoms sel range 20
> show #!19 models
> hide #!28 models
> paulunclip
> volume zone #19 nearAtoms sel range 30
> volume zone #19 nearAtoms sel range 30 newMap true
Opened cryosparc_P17_J62_004_volume_map.mrc zone as #29, grid size
512,512,512, pixel 0.834, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/codon_zone_P17_J62_004_volume_map.mrc models #29
> hide #!29 models
> show #!28 models
> paulclip
Changed 611738 atom styles
> hide #!28 models
> show #!27 models
> paulunclip
> select clear
> hide #13,17#!1-2,15 atoms
> volume #27 level 0.02816
> volume #27 level 0.02
> show #!29 models
> hide #!27 models
> volume #29 level 0.02
> hide #!29 models
> show #!28 models
> show #!14 models
> hide #!14 models
> color zone #28 near #15,1,2
[Repeated 1 time(s)]
> color zone #28 near #15,1,2 distance 5
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J117_005_volume_map_sharp.mrc
Opened cryosparc_P17_J117_005_volume_map_sharp.mrc as #30, grid size
512,512,512, pixel 0.834, shown at level 0.118, step 1, values float32
> hide #!28 models
> color #30 #b2b2b2
> show #13,17#!1-2,15 atoms
> hh
> paulclip
Changed 611738 atom styles
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J174_003_volume_map.mrc
Opened cryosparc_P17_J174_003_volume_map.mrc as #31, grid size 512,512,512,
pixel 0.834, shown at level 0.185, step 1, values float32
> hide #!30 models
> hide #!2 models
> show #!20 models
> show #!21 models
> paulclip
Changed 611738 atom styles
> cofron
> volume #31 level 0.09598
> volume #31 level 0.07924
> volume #31 level 0.0943
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J175_003_volume_map.mrc
Opened cryosparc_P17_J175_003_volume_map.mrc as #32, grid size 512,512,512,
pixel 0.834, shown at level 0.185, step 1, values float32
> paulclip
Changed 611738 atom styles
> hide #!31 models
> volume #32 level 0.1203
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J177_003_volume_map.mrc
Opened cryosparc_P17_J177_003_volume_map.mrc as #33, grid size 512,512,512,
pixel 0.834, shown at level 0.194, step 1, values float32
> hide #!32 models
> paulclip
Changed 611738 atom styles
> volume #33 level 0.1428
> volume #33 level 0.09634
> volume #33 level 0.1999
> hide #!33 models
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J178_003_volume_map.mrc
Opened cryosparc_P17_J178_003_volume_map.mrc as #34, grid size 512,512,512,
pixel 0.834, shown at level 0.195, step 1, values float32
> paulclip
Changed 611738 atom styles
> volume #34 level 0.1042
> hide #!34 models
> show #!31 models
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J180_003_volume_map.mrc
Opened cryosparc_P17_J180_003_volume_map.mrc as #35, grid size 512,512,512,
pixel 0.834, shown at level 0.187, step 1, values float32
> hide #!31 models
> paulclip
Changed 611738 atom styles
> volume #35 level 0.1249
> volume #35 level 0.09617
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J182_003_volume_map.mrc
Opened cryosparc_P17_J182_003_volume_map.mrc as #36, grid size 512,512,512,
pixel 0.834, shown at level 0.188, step 1, values float32
> hide #!35 models
> paulclip
Changed 611738 atom styles
> volume #36 level 0.1141
> volume #36 level 0.08376
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J184_002_volume_map.mrc
Opened cryosparc_P17_J184_002_volume_map.mrc as #37, grid size 512,512,512,
pixel 0.834, shown at level 0.186, step 1, values float32
> hide #!36 models
> paulclip
Changed 611738 atom styles
> volume #37 level 0.09564
> show #!31 models
> hide #!37 models
> hide #!31 models
> show #!36 models
> show #!35 models
> hide #!36 models
> show #!36 models
> hide #!35 models
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J186_003_volume_map.mrc
Opened cryosparc_P17_J186_003_volume_map.mrc as #38, grid size 512,512,512,
pixel 0.834, shown at level 0.187, step 1, values float32
> paulclip
Changed 611738 atom styles
> hide #!36 models
> volume #38 level 0.1207
> volume #38 level 0.114
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/cryosparc_P17_J114_003_volume_map.mrc
Opened cryosparc_P17_J114_003_volume_map.mrc as #39, grid size 512,512,512,
pixel 0.834, shown at level 0.205, step 1, values float32
> close #22-36
> paulclip
Changed 611738 atom styles
> hide #!38 models
> hide #!20 models
> hide #!21 models
> show #!8 models
> volume #39 level 0.1197
> paulunclip
> show #!11 models
> hide #!11 models
> fitmap #8 inMap #39
Fit molecule PreH2_PE-tRNA_8GLP.cif (#8) to map
cryosparc_P17_J114_003_volume_map.mrc (#39) using 1645 atoms
average map value = 0.07789, steps = 72
shifted from previous position = 0.856
rotated from previous position = 2.93 degrees
atoms outside contour = 1181, contour level = 0.11968
Position of PreH2_PE-tRNA_8GLP.cif (#8) relative to
cryosparc_P17_J114_003_volume_map.mrc (#39) coordinates:
Matrix rotation and translation
0.99995160 -0.00776540 0.00604111 -4.94526519
0.00773348 0.99995611 0.00528889 0.79479294
-0.00608191 -0.00524192 0.99996777 9.64129459
Axis -0.47185853 0.54320128 0.69446519
Axis point 561.37965259 -65.45752298 0.00000000
Rotation angle (degrees) 0.63936915
Shift along axis 9.46074158
> paulambience
> volume zone #39 nearAtoms #8 range 5
> volume zone #39 nearAtoms #8 range 4
> volume zone #39 nearAtoms #8 range 4 newMap true
Opened cryosparc_P17_J114_003_volume_map.mrc zone as #22, grid size
512,512,512, pixel 0.834, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/E-tRNA_zone_P17_J114.mrc models #22
> hide #!22 models
> show #!39 models
> volume unzone
> open
> /Users/psauer/Documents/Processing/reference_PDBs/RNC_indiv_ref_models/mRNA_8GLP.cif
Chain information for mRNA_8GLP.cif #23
---
Chain | Description
mR | mRNA
> hide #!39 models
> select add #23
258 atoms, 278 bonds, 8 residues, 1 model selected
> hh
> paulclip
Changed 611996 atom styles
> show #!39 models
> hide #!39 models
> show #!19 models
> hide #!8 models
> show #!2 models
> volume #19 level 0.09781
> ui mousemode right "translate selected models"
> view matrix models #23,1,0,0,-4.2836,0,1,0,5.0466,0,0,1,6.3397
> hide #!19 models
> select #23/mR:37@C1'
1 atom, 1 residue, 1 model selected
> select add #23/mR:38@C1'
2 atoms, 2 residues, 1 model selected
> select up
4 atoms, 1 bond, 3 residues, 1 model selected
> select up
97 atoms, 104 bonds, 3 residues, 1 model selected
> show #!19 models
> fitmap sel inMap #19
Fit molecule mRNA_8GLP.cif (#23) to map cryosparc_P17_J62_004_volume_map.mrc
(#19) using 97 atoms
average map value = 0.1036, steps = 68
shifted from previous position = 1.25
rotated from previous position = 6.18 degrees
atoms outside contour = 43, contour level = 0.097809
Position of mRNA_8GLP.cif (#23) relative to
cryosparc_P17_J62_004_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99460544 0.07092831 0.07569146 -38.55030893
-0.07308806 0.99698254 0.02615228 15.13683087
-0.07360813 -0.03154334 0.99678827 30.61075162
Axis -0.26796112 0.69340588 -0.66886855
Axis point 395.65535300 0.00000000 536.26313268
Rotation angle (degrees) 6.18025254
Shift along axis 0.35138239
> select clear
> save /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/1289_myc_session.cxs includeMaps true
——— End of log from Thu Oct 17 14:08:33 2024 ———
opened ChimeraX session
> hide #!19 models
> show #!19 models
> hide #17 models
> show #17 models
> hide #23 models
> show #23 models
> hide #23 models
> hide #!15 models
> show #!15 models
> hide #13 models
> hide #!15 models
> hide #17 models
> hide #!2 models
> hide #!1 models
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/PDB_deposition/IDB-001_MYC_model_refined_034.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
PS2_IDB-1289/PDB_deposition/IDB-001_MYC_model_refined_034.cif
---
warnings | Unknown polymer entity '1' on line 459
Unknown polymer entity '2' on line 81626
Unknown polymer entity '3' on line 84273
Unknown polymer entity '4' on line 87615
Unknown polymer entity '5' on line 89670
77 messages similar to the above omitted
Expected gap or linking atom in HY3 /SX:62 for GLN /SX:61
Expected gap or linking atom in HY3 /SX:62 for ASN /SX:63
Atom N3 is not in the residue template for IDB /L5:5700
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for IDB-001_MYC_model_refined_034.cif #24
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
NC | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
mR | No description available
42 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> color #!24 byhetero
> paulvis #24
Changed 219534 atom styles
> paulcolor #24
> hide #!19 models
> oo
> open
> /Users/psauer/Documents/Processing/ChimeraX_startup_preferences_Paul_20240911.cxc
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias hh hide H
> name roi (/Pt:74-end /NC:21-end /By:21-end /X /L5:4397,4398,4450,4451,4452,4531,4532,3905,3908,4449,3907,4399,4519,4548,5258,5294,5301,5303,5348,5374,5384,5208,5401,5394,5167) | (/Pt:74-end /NC:21-end /By:21-end /X /L5:4397,4398,4450,4451,4452,4531,4532,3905,3908,4449,3907,4399,4519,4548,5258,5294,5301,5303,5348,5374,5384,5208,5401,5394,5167) :<2.5 & :HOH
> name miniroi (/Pt:74-end /NC:21-end /By:21-end /X)
> name froi :3905,3907,3908,4397,4398,3909,4449,5167,5394,5258 :<2.5 & :HOH | (:3905,3907,3908,4397,4398,3909,4449,5167,5394,5258)
> name broi :4398,4399,4450,4451,4452,4519,4531,4532,4548,5401,5208,5374,5384,5348,5294,5301,5303 :<2.5 & :HOH | (:4398, 4399,4450,4451,4452,4519,4531,4532,4548,5401,5208,5374,5384,5348,5294,5301,5303)
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias paulclip cofr centerofview; style stick; surface cap false; clip near
> -2 far 8 position cofr; material transparentCastShadows false; lighting
> flat; graphics silhouettes false; transparency 60; volume step 1
> alias paulunclip ~clip; transparency 0; lighting soft; view all
> alias paulambience lighting fillInt 0.2 ambientInt 1.2 intensity 0.2
> multishadow 256 shadows false
> alias paullight material transparentCastShadows true; lighting soft;
> transparency 70; style stick; show cartoon; lighting intens 0.3
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; #disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.1; transparency 70;
> cofr centerofview; clip near -2 far 6 position cofr; #color ##~num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_30 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 30; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette ^RdYlBu-5;
> lighting soft; view all; transparency 0
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias paulvis lighting fillInt 0.2 ambientInt 1.2 intensity 0.2 multishadow
> 256 shadows false; material transparentcastshadows false; style $1 stick;
> transparency $1 60; nucleotides $1 atom; hide $1 cartoon; show $1 atoms;
> hide H; paulcolor $1
> alias paullabel label $* residues color black height 0.8 bgcolor
> rgba(100%,100%,100%,0.6); ~label :HOH; label $*:IDB* text IDB
> alias IDB view :IDB*; paulclip; volume step 1
> alias nucrib cartoon style nucleic xsect oval width 2 thick 2
> alias paulcolor color $*/m #e31a1c; color $*/s,t #a6cee3; color $*/L* &
> nucleic #1f78b4; color $*/L* & protein #a6cee3; color $*/S* & nucleic
> #ff7f00; color $*/S* & protein #fdbf6f; color $*/Pt* #33a02c; color $*/Et*
> #b2df8a; color $*/mR #e31a1c; color $*:ANM $*:IDB* yellow; color $*/By,NC
> #fb9a99; color $*:Mg,K,Zn byhetero; color $*:HOH byhetero
> alias center cofron; view $* clip t pad 0.5; select $*
> alias paulrenumber renumber $1/L5 &~ nucleic start 10000 rel f; renumber
> $1/L5:K start 5100 rel f; renumber $1/L5:MG start 5300 rel f; renumber $1/L5
> & ligand start 5600 rel f; renumber $1/L5:IDB start 5700 rel f; renumber
> $1/L5:HOH start 6000 rel f
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_30
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"
> buttonpanel Shortcuts add IDB command IDB
> buttonpanel Shortcuts add paulvis command "paulvis #*"
> buttonpanel Shortcuts add paullabel command paullabel
> buttonpanel Shortcuts add paulclip command paulclip
> buttonpanel Shortcuts add paullight command paullight
> buttonpanel Shortcuts add paulsave command paulsave
> buttonpanel Shortcuts add unclip command paulunclip
> buttonpanel Shortcuts add paulambience command paulambience
> buttonpanel Shortcuts add paulstyle command paulstyle
> buttonpanel Shortcuts add delete_selected command "delete sel"
executed ChimeraX_startup_preferences_Paul_20240911.cxc
> paulcolor #24
> show #!19 models
> altlocs list
83923 residues have no alternate locations
TI-Post_SSU_8GLP.cif #1/SN HIS 123 has alternate locations A and B (using A)
TI-Post_SSU_8GLP.cif #1/ST TYR 48 has alternate locations A, B, and C (using
C)
TI-Post_SSU_8GLP.cif #1/Sa ARG 85 has alternate locations A and B (using A)
SSU_7LS2.cif #6/F3 ARG 85 has alternate locations A and B (using A)
PreH2_SSU_8GLP.cif #7/SN HIS 123 has alternate locations A and B (using A)
PreH2_SSU_8GLP.cif #7/ST TYR 48 has alternate locations A, B, and C (using C)
PreH2_SSU_8GLP.cif #7/Sa ARG 85 has alternate locations A and B (using A)
PreH1_SSU_8GLP.cif #10/SN HIS 123 has alternate locations A and B (using A)
PreH1_SSU_8GLP.cif #10/ST TYR 48 has alternate locations A, B, and C (using C)
PreH1_SSU_8GLP.cif #10/Sa ARG 85 has alternate locations A and B (using A)
LSU_8GLP.cif #15/L5 A 3908 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LA ARG 245 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LF ARG 62 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LF ARG 66 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LL ARG 190 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LP HIS 93 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LT LYS 36 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LT ARG 142 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LZ ARG 111 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Le ARG 33 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Lj HIS 66 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Lm ASN 120 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Lo HIS 90 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Lp ARG 85 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Lr LYS 84 has alternate locations A and B (using A)
LSU_7LS2.cif #16/A1 ARG 92 has alternate locations A and B (using A)
LSU_7LS2.cif #16/B1 ARG 137 has alternate locations A and B (using A)
IDB-001_MYC_model_refined_034.cif #24/L5 A 3908 has alternate locations A and
B (using B)
IDB-001_MYC_model_refined_034.cif #24/L5 U 4399 has alternate locations A and
B (using A)
>
Unknown command: altlocs #24 show
> altlocs show #24
> hide #!19 models
> paulcolor #24
> show #!19 models
> set bgColor white
> hide #!19 models
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/PDB_deposition/LSU_local-
> ref_maps/cryosparc_P17_J168_007_volume_map_sharp.mrc
Opened cryosparc_P17_J168_007_volume_map_sharp.mrc as #25, grid size
512,512,512, pixel 0.834, shown at level 0.12, step 1, values float32
> paulclip
Changed 831614 atom styles
> volume #25 level 0.107
> close #25
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/PDB_deposition/LSU_local-ref_maps/J168_007_volume_map.mrc
Opened J168_007_volume_map.mrc as #25, grid size 512,512,512, pixel 0.834,
shown at level 0.0732, step 1, values float32
> paulclip
Changed 831614 atom styles
> color #24 #b2b2b2
> color #25 #b2b2b2
> paulvis #24
Changed 219618 atom styles
> color #24/NC #24:IDB byhetero
> volume #25 level 0.07024
> save /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/1289_myc_session.cxs includeMaps true
> view v1
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/PDB_deposition/consenus_maps/cryosparc_P17_J117_005_volume_map.mrc
Opened cryosparc_P17_J117_005_volume_map.mrc as #26, grid size 512,512,512,
pixel 0.834, shown at level 0.0846, step 1, values float32
> show #!39 models
> hide #!39 models
> hide #!25 models
> hide #!24 models
> volume #26 level 0.08197
> color #26 #b2b2b2
> volume #26 level 0.07668
> save /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/1289_myc_session.cxs includeMaps true
> show #!24 models
> hide #!26 models
> view v9
Expected an objects specifier or a view name or a keyword
> view list
Named views: v1, v2, v3, v4, v5, v6, v7, v8
> view v2
> view v3
> view v4
> view v5
> view v6
> view v7
> view v8
> view
> paulclip
Changed 831614 atom styles
> cofron
> paulambience
> show #!25 models
> cofroff
> ui tool show "Side View"
> view name v9
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> hide #!25 models
> show #!25 models
> save /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/1289_myc_session.cxs includeMaps true
——— End of log from Mon Jun 16 13:37:56 2025 ———
opened ChimeraX session
> view v1
> hide #!24 models
> transparency 0
> open /Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
> PS2/PDB_deposition/consensus_maps/J106_003_volume_map.mrc
Opened J106_003_volume_map.mrc as #27, grid size 512,512,512, pixel 0.834,
shown at level 0.0839, step 1, values float32
> hide #!25 models
> open /Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
> PS2/PDB_deposition/LSU_local-ref_maps/J110_004_volume_map.mrc
Opened J110_004_volume_map.mrc as #28, grid size 512,512,512, pixel 0.834,
shown at level 0.0803, step 1, values float32
> fitmap #28 inMap #27
Fit map J110_004_volume_map.mrc in map J106_003_volume_map.mrc using 1340912
points
correlation = 0.9895, correlation about mean = 0.9061, overlap = 2.304e+04
steps = 60, shift = 2.15, angle = 0.398 degrees
Position of J110_004_volume_map.mrc (#28) relative to J106_003_volume_map.mrc
(#27) coordinates:
Matrix rotation and translation
0.99997603 0.00172716 -0.00670539 -0.45616951
-0.00173115 0.99999833 -0.00058907 1.78679840
0.00670436 0.00060066 0.99997735 -0.61929998
Axis 0.08559515 -0.96476321 -0.24880801
Axis point 151.91496078 0.00000000 -48.03689072
Rotation angle (degrees) 0.39819544
Shift along axis -1.60879645
> open /Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
> PS2/PDB_deposition/noIDB_MYC_model_refined_060.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
PS2/PDB_deposition/noIDB_MYC_model_refined_060.cif
---
warnings | Unknown polymer entity '1' on line 463
Unknown polymer entity '2' on line 80137
Unknown polymer entity '3' on line 82726
Unknown polymer entity '4' on line 86126
Unknown polymer entity '5' on line 88141
77 messages similar to the above omitted
Expected gap or linking atom in HY3 /SX:62 for GLN /SX:61
Expected gap or linking atom in HY3 /SX:62 for ASN /SX:63
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for noIDB_MYC_model_refined_060.cif #29
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
NC | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
mR | No description available
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> paulvis #29
Changed 216956 atom styles
> hide #!27 models
> paulclip
Changed 1048570 atom styles
> set bgColor black
> cofron
> hide #!28 models
> hide /NC pbonds
> color #29/NC byhetero
> show #!24 models
> hide #!24 models
> hide #!29 models
> show #!27 models
> show #!28 models
> paulunclip
> show #!25 models
> fitmap #27 inMap #25 bring #28
Expected a keyword
> fitmap #27 inMap #25
Fit map J106_003_volume_map.mrc in map J168_007_volume_map.mrc using 1341680
points
correlation = 0.9828, correlation about mean = 0.8469, overlap = 2.029e+04
steps = 116, shift = 10.1, angle = 2.78 degrees
Position of J106_003_volume_map.mrc (#27) relative to J168_007_volume_map.mrc
(#25) coordinates:
Matrix rotation and translation
0.99902160 0.04142954 0.01547379 -17.45700528
-0.04173144 0.99893412 0.01972587 9.45124859
-0.01464006 -0.02035231 0.99968568 14.81022136
Axis -0.41274184 0.31012504 -0.85642667
Axis point 233.85836592 452.26905346 0.00000000
Rotation angle (degrees) 2.78286949
Shift along axis -2.54756326
> fitmap #28 inMap #25
Fit map J110_004_volume_map.mrc in map J168_007_volume_map.mrc using 1340912
points
correlation = 0.9848, correlation about mean = 0.8717, overlap = 2.007e+04
steps = 116, shift = 10.2, angle = 2.77 degrees
Position of J110_004_volume_map.mrc (#28) relative to J168_007_volume_map.mrc
(#25) coordinates:
Matrix rotation and translation
0.99904168 0.04295074 0.00842356 -17.76107338
-0.04310741 0.99888218 0.01939451 11.19514232
-0.00758114 -0.01973904 0.99977642 14.06678138
Axis -0.40813767 0.16691867 -0.89753095
Axis point 261.54715363 452.68963866 0.00000000
Rotation angle (degrees) 2.74790519
Shift along axis -3.50773019
> fitmap #29 inMap #25
Fit molecule noIDB_MYC_model_refined_060.cif (#29) to map
J168_007_volume_map.mrc (#25) using 216956 atoms
average map value = 0.1037, steps = 116
shifted from previous position = 10
rotated from previous position = 2.78 degrees
atoms outside contour = 65160, contour level = 0.070239
Position of noIDB_MYC_model_refined_060.cif (#29) relative to
J168_007_volume_map.mrc (#25) coordinates:
Matrix rotation and translation
0.99902469 0.04138589 0.01539109 -17.43890994
-0.04168711 0.99893463 0.01979370 9.42400854
-0.01455552 -0.02041601 0.99968561 14.79494227
Axis -0.41440661 0.30863375 -0.85616141
Axis point 233.25034631 452.21856415 0.00000000
Rotation angle (degrees) 2.78078491
Shift along axis -2.53149199
> show #!29 models
> show #!24 models
> hide #!25 models
> hide #!27 models
> hide #!28 models
> mmaker #29 to #24 bring #27,28
Specify a single 'to' model only
> mmaker #29 to #24 bring #27,#28
> matchmaker #29 to #24 bring #27,#28
Invalid "bring" argument: only initial part "#27" of atom specifier valid
> mmaker #29 to #24 bring #27-28
Specify a single 'to' model only
> mmaker #29 to #24 bring #27
Specify a single 'to' model only
> mmaker #29 to #24 bring #27
Specify a single 'to' model only
> mmaker #29 to #24.1 bring #27
No 'to' model specified
> mmaker #29 to #24
Specify a single 'to' model only
> hide #!24 models
> show #!24 models
> hide #!29 models
> show #!29 models
> mmaker #29 to #24.1
No 'to' model specified
> mmaker #29 to #24.2
No 'to' model specified
> mmaker #29 to #24.4
Specify a single 'to' model only
> mmaker #29 to #24.3
No 'to' model specified
>
Incomplete command: altlocs
> altlocs hide
> mmaker #29 to #24.3
No 'to' model specified
> mmaker #29 to #24
Specify a single 'to' model only
> mmaker #29 to #24.4.1
Specify a single 'to' model only
> mmaker #29 to #24.4.1.1
No matrix compatible with both reference structure and all match structures
> mmaker #29 to #24.4.1.2
No matrix compatible with both reference structure and all match structures
> altlocs list
106212 residues have no alternate locations
TI-Post_SSU_8GLP.cif #1/SN HIS 123 has alternate locations A and B (using A)
TI-Post_SSU_8GLP.cif #1/ST TYR 48 has alternate locations A, B, and C (using
C)
TI-Post_SSU_8GLP.cif #1/Sa ARG 85 has alternate locations A and B (using A)
SSU_7LS2.cif #6/F3 ARG 85 has alternate locations A and B (using A)
PreH2_SSU_8GLP.cif #7/SN HIS 123 has alternate locations A and B (using A)
PreH2_SSU_8GLP.cif #7/ST TYR 48 has alternate locations A, B, and C (using C)
PreH2_SSU_8GLP.cif #7/Sa ARG 85 has alternate locations A and B (using A)
PreH1_SSU_8GLP.cif #10/SN HIS 123 has alternate locations A and B (using A)
PreH1_SSU_8GLP.cif #10/ST TYR 48 has alternate locations A, B, and C (using C)
PreH1_SSU_8GLP.cif #10/Sa ARG 85 has alternate locations A and B (using A)
LSU_8GLP.cif #15/L5 A 3908 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LA ARG 245 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LF ARG 62 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LF ARG 66 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LL ARG 190 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LP HIS 93 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LT LYS 36 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LT ARG 142 has alternate locations A and B (using A)
LSU_8GLP.cif #15/LZ ARG 111 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Le ARG 33 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Lj HIS 66 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Lm ASN 120 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Lo HIS 90 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Lp ARG 85 has alternate locations A and B (using A)
LSU_8GLP.cif #15/Lr LYS 84 has alternate locations A and B (using A)
LSU_7LS2.cif #16/A1 ARG 92 has alternate locations A and B (using A)
LSU_7LS2.cif #16/B1 ARG 137 has alternate locations A and B (using A)
IDB-001_MYC_model_refined_034.cif #!24/L5 A 3908 has alternate locations A and
B (using B)
IDB-001_MYC_model_refined_034.cif #!24/L5 U 4399 has alternate locations A and
B (using A)
A #24.4.1.1/L5 A 3908 has alternate locations A (using A)
B #24.4.1.2/L5 A 3908 has alternate locations B (using B)
A #24.4.2.1/L5 U 4399 has alternate locations A (using A)
B #24.4.2.2/L5 U 4399 has alternate locations B (using B)
noIDB_MYC_model_refined_060.cif #29/L5 A 3908 has alternate locations A and B
(using B)
> mmaker #29 to #24
Specify a single 'to' model only
> close #24
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/PDB_deposition/IDB-001_MYC_model_refined_034.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
PS2_IDB-1289/PDB_deposition/IDB-001_MYC_model_refined_034.cif
---
warnings | Unknown polymer entity '1' on line 459
Unknown polymer entity '2' on line 81626
Unknown polymer entity '3' on line 84273
Unknown polymer entity '4' on line 87615
Unknown polymer entity '5' on line 89670
77 messages similar to the above omitted
Expected gap or linking atom in HY3 /SX:62 for GLN /SX:61
Expected gap or linking atom in HY3 /SX:62 for ASN /SX:63
Atom N3 is not in the residue template for IDB /L5:5700
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for IDB-001_MYC_model_refined_034.cif #24
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
NC | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
mR | No description available
42 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> paulvis #24
Changed 219534 atom styles
> mmaker #29 to #24
Computing secondary structure
[Repeated 1 time(s)] 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 IDB-001_MYC_model_refined_034.cif, chain L5 (#24) with
noIDB_MYC_model_refined_060.cif, chain L5 (#29), sequence alignment score =
21504.6
RMSD between 3546 pruned atom pairs is 0.357 angstroms; (across all 3546
pairs: 0.357)
> paulclip
Changed 1048486 atom styles
> color /NC :IDB byhetero
> color #24/NC #24:IDB byhetero
> hide :HOH,MG atoms
> morph #29/L5,NC #24/L5,NC
Computed 51 frame morph #30
> coordset #30 1,51
> show #!24 models
> hide #!30 models
> show #!29 models
> hide #!24 models
> show #!27 models
> show #!28 models
> color #28 #b2b2b2
> volume #28 level 0.06072
> volume #28 level 0.0617
> altlocs show
> hide #!29 models
> show #!30 models
> show #!24 models
> hide #!30 models
> show #!29 models
> hide #!24 models
> open /Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
> PS2/modeling_intermediates/noIDB_MYC_model_refined_060_altconf-coot.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
PS2/modeling_intermediates/noIDB_MYC_model_refined_060_altconf-coot.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 19
Unknown polymer entity '1' on line 114
Unknown polymer entity '2' on line 79828
Unknown polymer entity '3' on line 82417
Unknown polymer entity '4' on line 85817
Unknown polymer entity '5' on line 87832
77 messages similar to the above omitted
Expected gap or linking atom in AME /SV:1 for GLN /SV:2
Expected gap or linking atom in HY3 /SX:62 for GLN /SX:61
Expected gap or linking atom in HY3 /SX:62 for ASN /SX:63
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for noIDB_MYC_model_refined_060_altconf-coot.cif #31
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
NC | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
mR | No description available
62 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> paulvis #31
Changed 216956 atom styles
> mmaker #31 to #24
Specify a single 'to' model only
> hide #!29 models
> mmaker #31 to #29
Specify a single 'to' model only
> fitmap #31 inMap #28
Fit molecule noIDB_MYC_model_refined_060_altconf-coot.cif (#31) to map
J110_004_volume_map.mrc (#28) using 216956 atoms
average map value = 0.1163, steps = 136
shifted from previous position = 12.1
rotated from previous position = 2.75 degrees
atoms outside contour = 39598, contour level = 0.061703
Position of noIDB_MYC_model_refined_060_altconf-coot.cif (#31) relative to
J110_004_volume_map.mrc (#28) coordinates:
Matrix rotation and translation
1.00000000 0.00002387 0.00001393 -0.00757906
-0.00002387 1.00000000 0.00004183 0.00256068
-0.00001393 -0.00004183 1.00000000 0.00420096
Axis -0.83436328 0.27781157 -0.47608680
Axis point 0.00000000 157.73323406 -27.77152504
Rotation angle (degrees) 0.00287251
Shift along axis 0.00503505
> hide /NC pbonds
> hide #!28 models
> select clear
> select #31/Pt:75@O3'
1 atom, 1 residue, 1 model selected
> select add #31/NC:31@C
2 atoms, 2 residues, 1 model selected
> bond sel
Created 1 bond
> color #31/NC byhetero
> show #!24 models
> mmaker #31 to #24
Specify a single 'to' model only
> mmaker #31/L5 to #24/L5
Specify a single 'to' model only
> mmaker #31/L5 to #24.4.1.1/L5
No matrix compatible with both reference structure and all match structures
> mmaker #31/L5 to #24.4.1/L5
Specify a single 'to' model only
> mmaker #31/Pt to #24/Pt
No matrix compatible with both reference structure and all match structures
> close #24
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/PDB_deposition/IDB-001_MYC_model_refined_034.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
PS2_IDB-1289/PDB_deposition/IDB-001_MYC_model_refined_034.cif
---
warnings | Unknown polymer entity '1' on line 459
Unknown polymer entity '2' on line 81626
Unknown polymer entity '3' on line 84273
Unknown polymer entity '4' on line 87615
Unknown polymer entity '5' on line 89670
77 messages similar to the above omitted
Expected gap or linking atom in HY3 /SX:62 for GLN /SX:61
Expected gap or linking atom in HY3 /SX:62 for ASN /SX:63
Atom N3 is not in the residue template for IDB /L5:5700
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for IDB-001_MYC_model_refined_034.cif #24
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
NC | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
mR | No description available
42 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> paulvis #24
Changed 219534 atom styles
> mmaker #31 to #24
Computing secondary structure
[Repeated 2 time(s)] 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 IDB-001_MYC_model_refined_034.cif, chain L5 (#24) with
noIDB_MYC_model_refined_060_altconf-coot.cif, chain L5 (#31), sequence
alignment score = 21504.6
RMSD between 3546 pruned atom pairs is 0.357 angstroms; (across all 3546
pairs: 0.357)
> paulcolor #31
> hide #!24 models
> select clear
> select #31/NC:8-12
132 atoms, 142 bonds, 10 residues, 1 model selected
> select #31/NC & nucleic
Nothing selected
> select #31/NC
1718 atoms, 1898 bonds, 1 pseudobond, 96 residues, 2 models selected
> select subtract protein
2 atoms, 2 residues, 1 model selected
> select #31/Pt
4 atoms, 4 residues, 1 model selected
> select #31/NC
1718 atoms, 1898 bonds, 1 pseudobond, 96 residues, 2 models selected
> select subtract #31@@serial_number=139652
1717 atoms, 1894 bonds, 1 pseudobond, 96 residues, 2 models selected
> select subtract #31@@serial_number=139668
1716 atoms, 1891 bonds, 1 pseudobond, 96 residues, 2 models selected
> select subtract #31@@serial_number=139693
1715 atoms, 1887 bonds, 1 pseudobond, 96 residues, 2 models selected
> select subtract #31@@serial_number=139702
1714 atoms, 1884 bonds, 1 pseudobond, 96 residues, 2 models selected
> select clear
> open /Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
> PS2/modeling_intermediates/noIDB_MYC_model_refined_060_altconf-coot.cif
Summary of feedback from opening
/Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
PS2/modeling_intermediates/noIDB_MYC_model_refined_060_altconf-coot.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 19
Unknown polymer entity '1' on line 114
Unknown polymer entity '2' on line 79828
Unknown polymer entity '3' on line 82417
Unknown polymer entity '4' on line 85817
Unknown polymer entity '5' on line 87832
77 messages similar to the above omitted
Expected gap or linking atom in AME /SV:1 for GLN /SV:2
Expected gap or linking atom in HY3 /SX:62 for GLN /SX:61
Expected gap or linking atom in HY3 /SX:62 for ASN /SX:63
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for noIDB_MYC_model_refined_060_altconf-coot.cif #32
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
NC | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
mR | No description available
62 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!31 models
> show #!32 atoms
> show #!32 cartoons
Computing secondary structure
> style #!32 stick
Changed 216956 atom styles
> hide #!32 cartoons
> select #32/Pt:75@O3'
1 atom, 1 residue, 1 model selected
> select add #32/NC:31@C
2 atoms, 2 residues, 1 model selected
> bond sel
Created 1 bond
> close #32
> show #!31 models
> show #!24 models
> select #24/Pt
1600 atoms, 1780 bonds, 56 pseudobonds, 78 residues, 2 models selected
> select #24/Pt :<1 & #31
1600 atoms, 1780 bonds, 78 residues, 1 model selected
> changechains sel Pt
Cannot reassign chain ID to only part of polymeric chain
(noIDB_MYC_model_refined_060_altconf-coot.cif #31/NC)
> close #31
> show #!29 models
> color #24/NC #24:IDB byhetero
> show #!30 models
> hide #!29 models
> hide #!24 models
> lighting simple
> show #!24 models
> hide #!24 models
> show #!29 models
> hide #!29 models
> show #!28 models
> paulclip
Changed 1260582 atom styles
> volume #28 level 0.06758
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/PDB_deposition/LSU_local-
> ref_maps/cryosparc_P17_J168_007_volume_map_sharp.mrc
Opened cryosparc_P17_J168_007_volume_map_sharp.mrc as #31, grid size
512,512,512, pixel 0.834, shown at level 0.12, step 1, values float32
> paulclip
Changed 1260582 atom styles
> hide #!28 models
> close #31
> open /Users/psauer/Documents/Processing/20240530_IVTT15_RNC-
> PS2/PDB_deposition/LSU_local-
> ref_maps/cryosparc_P9_J110_004_volume_map_sharp.mrc
Opened cryosparc_P9_J110_004_volume_map_sharp.mrc as #31, grid size
512,512,512, pixel 0.834, shown at level 0.128, step 1, values float32
> fitmap #31 inMap #28
Fit map cryosparc_P9_J110_004_volume_map_sharp.mrc in map
J110_004_volume_map.mrc using 1337900 points
correlation = 0.9628, correlation about mean = 0.8209, overlap = 4.192e+04
steps = 152, shift = 12.3, angle = 2.75 degrees
Position of cryosparc_P9_J110_004_volume_map_sharp.mrc (#31) relative to
J110_004_volume_map.mrc (#28) coordinates:
Matrix rotation and translation
1.00000000 -0.00002539 0.00003802 -0.00439243
0.00002539 1.00000000 -0.00000601 -0.00114438
-0.00003802 0.00000601 1.00000000 0.01249798
Axis 0.13027347 0.82451055 0.55064614
Axis point 251.00106016 0.00000000 133.92363094
Rotation angle (degrees) 0.00264203
Shift along axis 0.00536619
> paulclip
Changed 1260582 atom styles
> hide #!31 models
> show #!28 models
> volume #28 level 0.05681
> show #!25 models
> paulunclip
> hide #!30 models
> volume #25 level 0.06423
> hide #!25 models
> show #!26 models
> show #!25 models
> hide #!25 models
> hide #!26 models
> show #!28 models
> volume #28 level 0.07247
> show #!27 models
> hide #!28 models
> view v1
> view v9
> show #!29 models
> hide #!27 models
> show #!28 models
> show #!27 models
> hide #!28 models
> hide #!27 models
> show #!30 models
> hide #!29 models
> show #!29 models
> hide #!30 models
> show #!31 models
> hide #!31 models
> show #!28 models
> show #!30 models
> hide #!29 models
> hide #!28 models
> select #30 & roi
391 atoms, 423 bonds, 2 pseudobonds, 22 residues, 2 models selected
> select clear
> set bgColor white
> lighting simple
> graphics quality 0
> lighting soft
> graphics quality 5
> paulambience
> show #24:IDB atoms
> show #!24 models
> hide #24 &~ :IDB atoms
> hide #!24 models
> save /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/1289_myc_session.cxs includeMaps true
> lighting simple
> graphics quality 0
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/MYC_RNC_+-IDB_movie_v10_commands.cxc
> show #24,29,30 atoms
> hide atoms
> hide cartoons
> hide H
> set bgColor white
> hide #* models
> ~clip
> cofroff
> transparency 0
> volume #25 level 0.0642
> volume #26 level 0.0767
> volume #28 level 0.0725
> volume #31 level 0.128
> coordset #30 1
> view v1
> cofroff
> show #27 models
> surface dust #27 size 1.5
> movie record supersample 3
> wait 20
> rock y 30 100 cycle 100
> wait 120
> view v9 50
> wait 47
> hide #27 models
> show #28 models
> transparency #28 60
> surface dust #28 size 1.5
> show #30 models
> show #30 atoms
> hh
> hide :MG,HOH,K atoms
> hide pbonds
> surface cap true
[Repeated 1 time(s)]
> wait 23
> rock y 30 100 cycle 100
> wait 120
> crossfade 20
> hide ~roi atoms
> hide #28 models
> wait 30
> rock y 30 100 cycle 100
> wait 120
> coordset #30 & roi
> hh
> wait 51
> crossfade 20
> show #24:IDB* atoms
> hh
> wait 40
> crossfade 20
> hide #24:IDB* atoms
> wait 20
> coordset #30 .,1
> wait 55
> coordset #30 & roi
> hh
> wait 51
> crossfade 20
> show #24:IDB* atoms
> hh
> wait 50
> movie stop
> movie encode output
> /Users/psauer/Documents/Processing/Comparison_all_compounds/comparison_all_stalled_RNCs_movie_v10.mp4
> framerate 15
Movie saved to
/Users/psauer/.../Comparison_all_compounds/comparison_all_stalled_RNCs_movie_v10.mp4
executed MYC_RNC_+-IDB_movie_v10_commands.cxc
> show #!24 models
> hide #24:IDB* atoms
> show #24:IDB* atoms
> view
> select #30 & broi
185 atoms, 200 bonds, 9 residues, 1 model selected
> select #30 & froi
151 atoms, 166 bonds, 7 residues, 1 model selected
> hide #30 & broi atoms
> coordset #30
> show #!28 models
> show #28 moderl
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #28 models
> view v9
> hide #28 models
> ~clip
> select clear
> view v9
> paulclip
Changed 1260582 atom styles
> surface cap false
> alias paulclip
Aliased "paulclip" to: cofr centerofview; style stick; surface cap false; clip
near -2 far 8 position cofr; material transparentCastShadows false; lighting
flat; graphics silhouettes false; transparency 60; volume step 1
> lighting soft
> lighting simple
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/MYC_RNC_+-IDB_movie_v10_commands.cxc
> show #24,29,30 atoms
> hide atoms
> hide cartoons
> hide H
> set bgColor white
> hide #* models
> ~clip
> cofroff
> transparency 0
> show #24,30 models
> hide atoms
> volume #25 level 0.0642
> volume #26 level 0.0767
> volume #28 level 0.0725
> volume #31 level 0.128
> coordset #30 1
> view v1
> cofroff
> show #27 models
> surface dust #27 size 1.5
> movie record supersample 3
> wait 20
> rock y 30 100 cycle 100
> wait 120
> view v9 50
> wait 47
> hide #27 models
> show #28 models
> transparency #28 60
> surface dust #28 size 1.5
> show #30 models
> show #30 atoms
> hh
> hide :MG,HOH,K atoms
> hide pbonds
> surface cap true
[Repeated 1 time(s)]
> wait 23
> rock y 30 100 cycle 100
> wait 120
> crossfade 20
> hide ~roi atoms
> hide #28 models
> hide #30 & broi atoms
> clip near -2 far 8 position cofr
> wait 30
> rock y 30 100 cycle 100
> wait 120
> coordset #30
> hh
> wait 51
> crossfade 20
> show #24:IDB* atoms
> hh
> wait 40
> crossfade 20
> hide #24:IDB* atoms
> wait 20
> coordset #30 .,1
> wait 55
> coordset #30
> hh
> wait 51
> crossfade 20
> show #24:IDB* atoms
> hh
> wait 50
> movie stop
> movie encode output
> /Users/psauer/Documents/Processing/Comparison_all_compounds/comparison_all_stalled_RNCs_movie_v10.mp4
Movie saved to
/Users/psauer/.../Comparison_all_compounds/comparison_all_stalled_RNCs_movie_v10.mp4
executed MYC_RNC_+-IDB_movie_v10_commands.cxc
> clip near -5 far 8 position cofr
> clip near -5 far 10 position cofr
> clip near -5 far 8 position cofr
> clip near 0 far 8 position cofr
> clip near 0 far 8
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/MYC_RNC_+-IDB_movie_v10_commands.cxc
> show #24,29,30 atoms
> hide atoms
> hide cartoons
> hide H
> set bgColor white
> hide #* models
> ~clip
> cofroff
> transparency 0
> show #24,30 models
> hide atoms
> volume #25 level 0.0642
> volume #26 level 0.0767
> volume #28 level 0.0725
> volume #31 level 0.128
> coordset #30 1
> view v1
> cofroff
> show #27 models
> surface dust #27 size 1.5
> movie record supersample 3
> wait 20
> rock y 30 100 cycle 100
> wait 120
> view v9 50
> wait 47
> hide #27 models
> show #28 models
> transparency #28 60
> surface dust #28 size 1.5
> show #30 models
> show #30 atoms
> hh
> hide :MG,HOH,K atoms
> hide pbonds
> surface cap true
> wait 23
> rock y 30 100 cycle 100
> wait 120
> crossfade 20
> hide ~roi atoms
> hide #28 models
> hide #30 & broi atoms
> clip near 0 far 8
> wait 30
> rock y 30 100 cycle 100
> wait 120
> coordset #30
> hh
> wait 51
> crossfade 20
> show #24:IDB* atoms
> hh
> wait 40
> crossfade 20
> hide #24:IDB* atoms
> wait 20
> coordset #30 .,1
> wait 55
> coordset #30
> hh
> wait 51
> crossfade 20
> show #24:IDB* atoms
> hh
> wait 50
> movie stop
> movie encode output
> /Users/psauer/Documents/Processing/Comparison_all_compounds/comparison_all_stalled_RNCs_movie_v10.mp4
Movie saved to
/Users/psauer/.../Comparison_all_compounds/comparison_all_stalled_RNCs_movie_v10.mp4
executed MYC_RNC_+-IDB_movie_v10_commands.cxc
> ui tool show "Side View"
> clip near 3 far 8
> clip near 0 far 8
> clip near 0 far 5
> clip near 0 far 10
> clip near 0 far 1
> clip near 5 far 1
> clip near -5 far 1
> clip near -5 far 8
> ~clip
> clip near far 8
Invalid "near" argument: Expected 'off' or a number
> clip far 8
> ~clip
> clip far 10
> ~clip
> clip far 15
> ~clip
> clip far 12
> open /Users/psauer/Documents/Processing/20241008_IVTT15_RNC-
> PS2_IDB-1289/MYC_RNC_+-IDB_movie_v10_commands.cxc
> show #24,29,30 atoms
> hide atoms
> hide cartoons
> hide H
> set bgColor white
> hide #* models
> ~clip
> cofroff
> transparency 0
> show #24,30 models
> hide atoms
> volume #25 level 0.0642
> volume #26 level 0.0767
> volume #28 level 0.0725
> volume #31 level 0.128
> coordset #30 1
> view v1
> cofroff
> show #27 models
> surface dust #27 size 1.5
> movie record supersample 3
> wait 20
> rock y 30 100 cycle 100
> wait 120
> view v9 50
> wait 47
> hide #27 models
> show #28 models
> transparency #28 60
> surface dust #28 size 1.5
> show #30 models
> show #30 atoms
> hh
> hide :MG,HOH,K atoms
> hide pbonds
> surface cap true
> wait 23
> rock y 30 100 cycle 100
> wait 120
> crossfade 20
> hide ~roi atoms
> hide #28 models
> hide #30 & broi atoms
> ~struts clip
> struts delete clip
Expected an atoms specifier or a keyword
> ~clip
> ~struts
[Repeated 1 time(s)]
> ~clip
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,6
Model Number: MNXA3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 64 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 1 day, 1 hour, 12 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2717D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NIHPresets: 1.2.7
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 5 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Command Line |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Ambiguous prefix chooses arbitrary command |
comment:2 by , 5 months ago
Hi Eric,
I see. This is easy to work with. Thank you for having a look!
Best
Paul
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Wednesday, June 18, 2025 at 11:36
To: Paul Sauer <psauer@interdictbio.com>, gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: meng@cgl.ucsf.edu <meng@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #18018: Ambiguous prefix chooses arbitrary command (was: ChimeraX bug report submission)
#18018: Ambiguous prefix chooses arbitrary command
-----------------------------------+------------------------
Reporter: psauer@… | Owner: Greg Couch
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Command Line | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------+------------------------
Changes (by pett):
* cc: pett, Elaine Meng (added)
* component: Unassigned => Command Line
* owner: (none) => Greg Couch
* platform: => all
* project: => ChimeraX
* status: new => assigned
* summary: ChimeraX bug report submission => Ambiguous prefix chooses
arbitrary command
Comment:
Hi Paul,
It's not exactly a bug per se. What the documentation means is
that to guarantee getting the right command you have to type at least
enough characters to disambiguate it from other commands. If you type
less, you get an arbitrary command that starts with those characters,
which probably isn't great, and we should change that behavior to generate
a message saying to type more characters, and showing what commands match
the characters you had typed so far.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18018#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
Note:
See TracTickets
for help on using tickets.
Hi Paul,
--Eric