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#9621 closed defect (duplicate)

Crash opening mmCIF file

Reported by:	tnguy028@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Input/Output	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description (last modified by pett)

The following bug report has been submitted:
Platform:        Linux-4.18.0-425.19.2.el8_7.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007efd11ffb700 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 316 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 574 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 1297 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007efebabcb740 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/mmcif/__init__.py", line 43 in open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 464 in collated_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/scratch/cs-bioinfo/tngu/6k_data/cif_box_crop_min.py", line 39 in main
  File "/scratch/cs-bioinfo/tngu/6k_data/cif_box_crop_min.py", line 50 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/scripting.py", line 61 in _exec_python
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/scripting.py", line 84 in open_python_script
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/runscript.py", line 38 in runscript
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> runscript /scratch/cs-bioinfo/tngu/6k_data/cif_box_crop_min.py --nogui

> wait

wait requires a frame count argument unless motion is in progress  

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 183,261,137,310,356,256

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

executed select_box.py  

> selectbox #1 inMap #2

Selected 21277 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_G.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_G.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_G.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_G.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 52598  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
52599  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
52600  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
52601  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
52602  
111 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
52851  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
52852  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
52853  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
52854  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
52855  
139 messages similar to the above omitted  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:48  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:48  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:220  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:307  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:376  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:410  
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:410  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:469  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:472  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:511  
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:511  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:637  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:837  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:858  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1662  
Atom ND1 has no neighbors to form bonds with according to residue template for
HIS /H:122  
Atom N has no neighbors to form bonds with according to residue template for
LYS /H:124  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /H:124  
Atom O has no neighbors to form bonds with according to residue template for
ALA /J:55  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /J:55  
Atom N has no neighbors to form bonds with according to residue template for
LYS /J:65  
Atom O has no neighbors to form bonds with according to residue template for
ARG /J:107  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /J:129  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /J:175  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /J:175  
Atom N has no neighbors to form bonds with according to residue template for
ALA /J:177  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /J:177  
Atom N has no neighbors to form bonds with according to residue template for
TYR /L:93  
Atom CB has no neighbors to form bonds with according to residue template for
TYR /L:93  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /L:103  
Atom CD has no neighbors to form bonds with according to residue template for
ARG /L:103  
Atom CB has no neighbors to form bonds with according to residue template for
ASN /W:80  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /W:80  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /W:105  
Atom N has no neighbors to form bonds with according to residue template for
LYS /W:124  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /W:124  
Atom O has no neighbors to form bonds with according to residue template for
LYS /p:711  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /p:711  
Atom N has no neighbors to form bonds with according to residue template for
VAL /q:191  
Atom O has no neighbors to form bonds with according to residue template for
LYS /q:203  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /q:203  
Atom O has no neighbors to form bonds with according to residue template for
LYS /q:204  
  
Chain information for 0057_6gsm_G.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
E | 40S ribosomal protein S4  
G | 40S ribosomal protein S6  
H | 40S ribosomal protein S7  
I | 40S ribosomal protein S8  
J | KLLA0E23673p  
L | KLLA0A10483p  
N | KLLA0F18040p  
W | 40S ribosomal protein S22  
Y | 40S ribosomal protein S24  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a  
p | Eukaryotic translation initiation factor 3 subunit B  
q | Eukaryotic translation initiation factor 3 subunit C  
s | Eukaryotic translation initiation factor 3 subunit I  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_G.mrc

Opened 0057_6gsm_G.mrc as #2, grid size 128,96,120, pixel 1, shown at level
0.137, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_G.cif (#1) to map 0057_6gsm_G.mrc (#2) using 21277
atoms  
average map value = 0.08241, steps = 52  
shifted from previous position = 0.565  
rotated from previous position = 0.0908 degrees  
atoms outside contour = 19986, contour level = 0.13743  
  
Position of 0057_6gsm_G.cif (#1) relative to 0057_6gsm_G.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999988 0.00036109 0.00033554 -0.46287238  
-0.00036159 0.99999880 0.00150641 -0.65958073  
-0.00033500 -0.00150654 0.99999881 0.32002281  
Axis -0.95041723 0.21151699 -0.22796416  
Axis point 0.00000000 246.46942257 469.98187871  
Rotation angle (degrees) 0.09081766  
Shift along axis 0.22745563  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_G_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 159,252,149,262,339,252

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 21101 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_E.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_E.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_E.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_E.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 52424  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
52425  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
52426  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
52427  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
52428  
129 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
52677  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
52678  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
52679  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
52680  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
52681  
151 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:24  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:135  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:157  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:157  
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:160  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:193  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:280  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:368  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:368  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:369  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:369  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:375  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:413  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:517  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:542  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:593  
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:593  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:594  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:594  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:629  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:633  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:633  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:633  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:717  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:717  
Atom N1 has no neighbors to form bonds with according to residue template for
G /2:720  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:720  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:826  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:826  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:859  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:962  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1659  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1716  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1716  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1717  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1717  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1735  
Atom O has no neighbors to form bonds with according to residue template for
ARG /C:179  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /C:179  
Atom N has no neighbors to form bonds with according to residue template for
HIS /G:81  
Atom CE1 has no neighbors to form bonds with according to residue template for
HIS /G:81  
Atom N has no neighbors to form bonds with according to residue template for
ARG /G:94  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /G:94  
Atom O has no neighbors to form bonds with according to residue template for
LYS /G:131  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /G:131  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /G:131  
Atom N has no neighbors to form bonds with according to residue template for
GLY /G:146  
Atom C has no neighbors to form bonds with according to residue template for
GLY /G:146  
Atom N has no neighbors to form bonds with according to residue template for
PRO /H:113  
Atom N has no neighbors to form bonds with according to residue template for
ARG /H:141  
Atom N has no neighbors to form bonds with according to residue template for
ARG /I:59  
Atom N has no neighbors to form bonds with according to residue template for
GLU /I:61  
Atom N has no neighbors to form bonds with according to residue template for
GLU /I:89  
Atom CB has no neighbors to form bonds with according to residue template for
GLU /I:89  
Atom O has no neighbors to form bonds with according to residue template for
ARG /J:40  
Atom N has no neighbors to form bonds with according to residue template for
SER /J:121  
Atom O has no neighbors to form bonds with according to residue template for
SER /J:121  
Atom OG has no neighbors to form bonds with according to residue template for
SER /J:121  
Atom N has no neighbors to form bonds with according to residue template for
SER /N:133  
Atom N has no neighbors to form bonds with according to residue template for
LEU /W:38  
Atom N has no neighbors to form bonds with according to residue template for
ALA /W:91  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /W:91  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLN /W:98  
Atom N has no neighbors to form bonds with according to residue template for
GLY /W:127  
Atom O has no neighbors to form bonds with according to residue template for
GLY /W:127  
Atom N has no neighbors to form bonds with according to residue template for
ASP /Y:3  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /p:472  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /p:472  
Atom O has no neighbors to form bonds with according to residue template for
THR /p:474  
Atom N has no neighbors to form bonds with according to residue template for
ASN /q:180  
Atom C has no neighbors to form bonds with according to residue template for
ASN /q:180  
  
Chain information for 0057_6gsm_E.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
C | KLLA0F09812p  
E | 40S ribosomal protein S4  
G | 40S ribosomal protein S6  
H | 40S ribosomal protein S7  
I | 40S ribosomal protein S8  
J | KLLA0E23673p  
L | KLLA0A10483p  
N | KLLA0F18040p  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S22  
X | KLLA0B11231p  
Y | 40S ribosomal protein S24  
p | Eukaryotic translation initiation factor 3 subunit B  
q | Eukaryotic translation initiation factor 3 subunit C  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_E.mrc

Opened 0057_6gsm_E.mrc as #2, grid size 104,88,104, pixel 1, shown at level
0.146, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_E.cif (#1) to map 0057_6gsm_E.mrc (#2) using 21101
atoms  
average map value = 0.08422, steps = 76  
shifted from previous position = 0.485  
rotated from previous position = 0.032 degrees  
atoms outside contour = 20281, contour level = 0.14627  
  
Position of 0057_6gsm_E.cif (#1) relative to 0057_6gsm_E.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999984 -0.00053731 -0.00015212 0.04774257  
0.00053731 0.99999986 0.00001714 -0.54367070  
0.00015211 -0.00001722 0.99999999 -0.22470372  
Axis -0.03075560 -0.27226867 0.96172962  
Axis point 1047.09390853 84.56971963 0.00000000  
Rotation angle (degrees) 0.03201084  
Shift along axis -0.06954807  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_E_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 149,210,183,228,289,278

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 17398 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_W.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_W.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_W.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_W.cif  
---  
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 48617  
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
48618  
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
48619  
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
48620  
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
48621  
131 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 48874  
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 48875  
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 48876  
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 48877  
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 48878  
179 messages similar to the above omitted  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:297  
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:298  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:349  
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:349  
Atom C3' has no neighbors to form bonds with according to residue template for
A /2:377  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:447  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:569  
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:665  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:668  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:772  
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:773  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:818  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:846  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:880  
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:880  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:946  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:974  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:975  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:975  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:976  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:976  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1053  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1063  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1065  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1066  
Atom C2' has no neighbors to form bonds with according to residue template for
C /2:1066  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1078  
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1294  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1770  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1786  
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:1787  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1789  
Atom N has no neighbors to form bonds with according to residue template for
LEU /A:24  
Atom O has no neighbors to form bonds with according to residue template for
LEU /A:24  
Atom N has no neighbors to form bonds with according to residue template for
ASP /A:43  
Atom C has no neighbors to form bonds with according to residue template for
ASP /A:43  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /A:43  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /A:127  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /A:127  
Atom O has no neighbors to form bonds with according to residue template for
ILE /A:173  
Atom CG has no neighbors to form bonds with according to residue template for
LEU /A:182  
Atom N has no neighbors to form bonds with according to residue template for
ALA /C:123  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /C:123  
Atom O has no neighbors to form bonds with according to residue template for
LYS /E:6  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /E:6  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /E:21  
Atom N has no neighbors to form bonds with according to residue template for
GLU /E:202  
Atom CG has no neighbors to form bonds with according to residue template for
GLU /E:202  
Atom CB has no neighbors to form bonds with according to residue template for
LEU /E:214  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /E:214  
Atom N has no neighbors to form bonds with according to residue template for
TYR /J:8  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /J:14  
Atom N has no neighbors to form bonds with according to residue template for
TYR /J:19  
Atom N has no neighbors to form bonds with according to residue template for
ARG /J:82  
Atom N has no neighbors to form bonds with according to residue template for
VAL /J:101  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /J:101  
Atom N has no neighbors to form bonds with according to residue template for
PHE /L:60  
Atom N has no neighbors to form bonds with according to residue template for
SER /L:65  
Atom N has no neighbors to form bonds with according to residue template for
VAL /L:76  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /L:76  
Atom O has no neighbors to form bonds with according to residue template for
VAL /L:107  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /L:114  
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /L:118  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /L:138  
Atom CE has no neighbors to form bonds with according to residue template for
LYS /N:27  
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /N:36  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /N:108  
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /N:108  
Atom O has no neighbors to form bonds with according to residue template for
LYS /N:109  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /N:109  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /N:138  
Atom N has no neighbors to form bonds with according to residue template for
ASN /N:151  
Atom O has no neighbors to form bonds with according to residue template for
ASN /X:65  
Atom N has no neighbors to form bonds with according to residue template for
ILE /X:117  
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /X:117  
Atom N has no neighbors to form bonds with according to residue template for
ASN /a:8  
Atom C has no neighbors to form bonds with according to residue template for
PHE /b:79  
  
Chain information for 0057_6gsm_W.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
A | 40S ribosomal protein S0  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
E | 40S ribosomal protein S4  
H | 40S ribosomal protein S7  
J | KLLA0E23673p  
L | KLLA0A10483p  
N | KLLA0F18040p  
R | KLLA0B01474p  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S22  
X | KLLA0B11231p  
a | 40S ribosomal protein S26  
b | 40S ribosomal protein S27  
q | Eukaryotic translation initiation factor 3 subunit C  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_W.mrc

Opened 0057_6gsm_W.mrc as #2, grid size 80,80,96, pixel 1, shown at level
0.151, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_W.cif (#1) to map 0057_6gsm_W.mrc (#2) using 17398
atoms  
average map value = 0.08231, steps = 44  
shifted from previous position = 0.389  
rotated from previous position = 0.0845 degrees  
atoms outside contour = 16885, contour level = 0.15092  
  
Position of 0057_6gsm_W.cif (#1) relative to 0057_6gsm_W.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999892 -0.00128029 -0.00071689 0.37524796  
0.00128019 0.99999917 -0.00014574 -0.48830710  
0.00071707 0.00014482 0.99999973 -0.43251942  
Axis 0.09852578 -0.48624862 0.86824821  
Axis point 420.03816705 300.52438078 0.00000000  
Rotation angle (degrees) 0.08448321  
Shift along axis -0.10112396  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_W_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 126,98,165,237,193,244

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 19007 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Q.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Q.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Q.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Q.cif  
---  
warnings | Invalid residue range for struct_conf "HELX7": invalid chain "E",
near line 50180  
Invalid residue range for struct_conf "HELX8": invalid chain "E", near line
50181  
Invalid residue range for struct_conf "HELX9": invalid chain "E", near line
50182  
Invalid residue range for struct_conf "HELX10": invalid chain "E", near line
50183  
Invalid residue range for struct_conf "HELX11": invalid chain "E", near line
50184  
149 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 8": invalid chain "E", near line
50434  
Invalid sheet range for struct_sheet_range "? 9": invalid chain "E", near line
50435  
Invalid sheet range for struct_sheet_range "? 10": invalid chain "E", near
line 50436  
Invalid sheet range for struct_sheet_range "? 11": invalid chain "E", near
line 50437  
Invalid sheet range for struct_sheet_range "? 12": invalid chain "E", near
line 50438  
147 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /1:24  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /1:24  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /1:25  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /1:25  
Atom OP1 has no neighbors to form bonds with according to residue template for
M2G /1:26  
Atom OP2 has no neighbors to form bonds with according to residue template for
M2G /1:26  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:906  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1005  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:1184  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1186  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1201  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1324  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1324  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1430  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1454  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1498  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1498  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1510  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1511  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1558  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1796  
Atom C has no neighbors to form bonds with according to residue template for
SER /D:6  
Atom CB has no neighbors to form bonds with according to residue template for
SER /D:6  
Atom N has no neighbors to form bonds with according to residue template for
LYS /D:10  
Atom C has no neighbors to form bonds with according to residue template for
LYS /D:10  
Atom C has no neighbors to form bonds with according to residue template for
ASP /D:14  
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /D:34  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /D:34  
Atom N has no neighbors to form bonds with according to residue template for
VAL /D:39  
Atom O has no neighbors to form bonds with according to residue template for
VAL /D:39  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /D:90  
Atom O has no neighbors to form bonds with according to residue template for
VAL /D:181  
Atom N has no neighbors to form bonds with according to residue template for
PHE /O:27  
Atom N has no neighbors to form bonds with according to residue template for
ALA /O:63  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /O:63  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /O:92  
Atom O has no neighbors to form bonds with according to residue template for
PRO /S:82  
Atom N has no neighbors to form bonds with according to residue template for
ARG /S:88  
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /S:98  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /S:98  
Atom N has no neighbors to form bonds with according to residue template for
ARG /S:110  
Atom N has no neighbors to form bonds with according to residue template for
PHE /S:128  
Atom CE3 has no neighbors to form bonds with according to residue template for
TRP /S:129  
Atom O has no neighbors to form bonds with according to residue template for
THR /U:104  
Atom C has no neighbors to form bonds with according to residue template for
ILE /U:106  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /a:38  
Atom N has no neighbors to form bonds with according to residue template for
SER /g:187  
Atom O has no neighbors to form bonds with according to residue template for
LEU /g:188  
Atom CB has no neighbors to form bonds with according to residue template for
LEU /g:232  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /g:232  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /g:232  
Atom N has no neighbors to form bonds with according to residue template for
ASN /i:96  
Atom OG has no neighbors to form bonds with according to residue template for
SER /j:4  
Atom N has no neighbors to form bonds with according to residue template for
GLU /j:38  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /j:62  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /l:172  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /l:214  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /l:214  
  
Chain information for 0057_6gsm_Q.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
A | 40S ribosomal protein S0  
D | KLLA0D08305p  
F | KLLA0D10659p  
O | 40S ribosomal protein S14  
P | KLLA0F07843p  
Q | 40S ribosomal protein S16  
R | KLLA0B01474p  
S | KLLA0B01562p  
T | KLLA0A07194p  
U | KLLA0F25542p  
Z | KLLA0B06182p  
a | 40S ribosomal protein S26  
c | 40S ribosomal protein S28  
d | 40S ribosomal protein S29  
g | KLLA0E12277p  
i | Eukaryotic translation initiation factor 1A  
j | Eukaryotic translation initiation factor 2 subunit alpha  
l | Eukaryotic translation initiation factor 2 subunit beta  
m | Eukaryotic translation initiation factor eIF-1  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Q.mrc

Opened 0057_6gsm_Q.mrc as #2, grid size 112,96,80, pixel 1, shown at level
0.131, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_Q.cif (#1) to map 0057_6gsm_Q.mrc (#2) using 19007
atoms  
average map value = 0.07351, steps = 44  
shifted from previous position = 0.452  
rotated from previous position = 0.238 degrees  
atoms outside contour = 18277, contour level = 0.13084  
  
Position of 0057_6gsm_Q.cif (#1) relative to 0057_6gsm_Q.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999819 -0.00178385 0.00066254 -0.03363365  
0.00178629 0.99999159 -0.00369093 0.32899231  
-0.00065595 0.00369211 0.99999297 -0.85139789  
Axis 0.88885447 0.15873590 0.42981467  
Axis point 0.00000000 190.79468520 103.47866224  
Rotation angle (degrees) 0.23795686  
Shift along axis -0.34361583  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Q_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 172,158,141,259,301,252

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 40820 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_2.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_2.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_2.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_2.cif  
---  
warnings | Invalid residue range for struct_conf "HELX72": invalid chain "P",
near line 72713  
Invalid residue range for struct_conf "HELX73": invalid chain "P", near line
72714  
Invalid residue range for struct_conf "HELX74": invalid chain "P", near line
72715  
Invalid residue range for struct_conf "HELX75": invalid chain "P", near line
72716  
Invalid residue range for struct_conf "HELX76": invalid chain "P", near line
72717  
21 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 79": invalid chain "P", near
line 72973  
Invalid sheet range for struct_sheet_range "? 80": invalid chain "P", near
line 72974  
Invalid sheet range for struct_sheet_range "? 95": invalid chain "W", near
line 72989  
Invalid sheet range for struct_sheet_range "? 96": invalid chain "W", near
line 72990  
Invalid sheet range for struct_sheet_range "? 97": invalid chain "W", near
line 72991  
75 messages similar to the above omitted  
Atom O2' has no neighbors to form bonds with according to residue template for
A /1:14  
Atom N6 has no neighbors to form bonds with according to residue template for
A /1:44  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:84  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:88  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:88  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:89  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:147  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:208  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:243  
Atom C6 has no neighbors to form bonds with according to residue template for
C /2:249  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:294  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:294  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:412  
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:451  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:451  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:453  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:535  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:642  
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:642  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:703  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:826  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:826  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:859  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:861  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:866  
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:866  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:877  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:886  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:895  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:895  
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:927  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:952  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:962  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:985  
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:985  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1068  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1166  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1168  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1168  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1174  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1201  
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1201  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1212  
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:1212  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1217  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1324  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1331  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1388  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1398  
Atom N1 has no neighbors to form bonds with according to residue template for
G /2:1407  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1407  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1453  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1489  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1593  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1600  
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:1653  
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1664  
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:1664  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1672  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1673  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1673  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1726  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1726  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1735  
Atom N has no neighbors to form bonds with according to residue template for
TYR /A:38  
Atom CE1 has no neighbors to form bonds with according to residue template for
TYR /A:81  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /A:81  
Atom N has no neighbors to form bonds with according to residue template for
PHE /A:102  
Atom C has no neighbors to form bonds with according to residue template for
PHE /A:102  
Atom N has no neighbors to form bonds with according to residue template for
SER /A:136  
Atom C has no neighbors to form bonds with according to residue template for
SER /A:136  
Atom OG has no neighbors to form bonds with according to residue template for
SER /A:136  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /A:140  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /A:140  
Atom N has no neighbors to form bonds with according to residue template for
VAL /A:156  
Atom C has no neighbors to form bonds with according to residue template for
ARG /B:115  
Atom O has no neighbors to form bonds with according to residue template for
VAL /B:150  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /B:150  
Atom CE1 has no neighbors to form bonds with according to residue template for
TYR /B:155  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /B:155  
Atom O has no neighbors to form bonds with according to residue template for
VAL /C:68  
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /C:155  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /D:11  
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /D:73  
Atom OG has no neighbors to form bonds with according to residue template for
SER /D:97  
Atom N has no neighbors to form bonds with according to residue template for
ARG /E:113  
Atom N has no neighbors to form bonds with according to residue template for
ILE /E:228  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /F:81  
Atom O has no neighbors to form bonds with according to residue template for
ASP /F:147  
Atom N has no neighbors to form bonds with according to residue template for
PRO /H:113  
Atom N has no neighbors to form bonds with according to residue template for
VAL /H:182  
Atom O has no neighbors to form bonds with according to residue template for
VAL /H:182  
Atom N has no neighbors to form bonds with according to residue template for
ASN /I:88  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /I:190  
Atom N has no neighbors to form bonds with according to residue template for
LEU /I:197  
Atom N has no neighbors to form bonds with according to residue template for
ARG /J:174  
Atom N has no neighbors to form bonds with according to residue template for
LYS /K:31  
Atom N has no neighbors to form bonds with according to residue template for
HIS /L:18  
Atom O has no neighbors to form bonds with according to residue template for
ILE /L:19  
Atom O has no neighbors to form bonds with according to residue template for
ARG /L:29  
Atom N has no neighbors to form bonds with according to residue template for
ALA /N:111  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /N:115  
Atom N has no neighbors to form bonds with according to residue template for
SER /N:133  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /O:70  
Atom NE has no neighbors to form bonds with according to residue template for
ARG /P:77  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /P:77  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /P:124  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /P:124  
Atom N has no neighbors to form bonds with according to residue template for
THR /R:8  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /R:8  
Atom N has no neighbors to form bonds with according to residue template for
ILE /U:86  
Atom C has no neighbors to form bonds with according to residue template for
ARG /Y:20  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /Y:53  
Atom N has no neighbors to form bonds with according to residue template for
TYR /Y:76  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /Y:82  
Atom O has no neighbors to form bonds with according to residue template for
LYS /Y:83  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /Y:83  
Atom N has no neighbors to form bonds with according to residue template for
SER /Y:124  
Atom OG has no neighbors to form bonds with according to residue template for
SER /Y:124  
Atom N has no neighbors to form bonds with according to residue template for
ALA /Y:126  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /Y:126  
Atom N has no neighbors to form bonds with according to residue template for
SER /a:54  
Atom OG has no neighbors to form bonds with according to residue template for
SER /a:54  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /b:25  
Atom N has no neighbors to form bonds with according to residue template for
PHE /c:32  
Atom O has no neighbors to form bonds with according to residue template for
GLU /c:58  
Atom N has no neighbors to form bonds with according to residue template for
ARG /h:23  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /j:47  
Atom N has no neighbors to form bonds with according to residue template for
GLN /j:60  
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:63  
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:96  
Atom N has no neighbors to form bonds with according to residue template for
ILE /l:230  
Atom NE has no neighbors to form bonds with according to residue template for
ARG /m:53  
Atom CG has no neighbors to form bonds with according to residue template for
GLU /m:76  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /m:76  
Atom CG has no neighbors to form bonds with according to residue template for
LEU /p:99  
Atom N has no neighbors to form bonds with according to residue template for
THR /p:123  
Atom O has no neighbors to form bonds with according to residue template for
THR /p:123  
Atom N has no neighbors to form bonds with according to residue template for
HIS /p:153  
Atom N has no neighbors to form bonds with according to residue template for
LYS /p:374  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /p:374  
Atom N has no neighbors to form bonds with according to residue template for
VAL /p:422  
Atom N has no neighbors to form bonds with according to residue template for
GLU /p:481  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /p:481  
Atom CB has no neighbors to form bonds with according to residue template for
GLU /q:101  
Atom N has no neighbors to form bonds with according to residue template for
ALA /q:177  
Atom C has no neighbors to form bonds with according to residue template for
ALA /q:177  
Atom N has no neighbors to form bonds with according to residue template for
LYS /q:189  
  
Chain information for 0057_6gsm_2.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
A | 40S ribosomal protein S0  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
D | KLLA0D08305p  
E | 40S ribosomal protein S4  
F | KLLA0D10659p  
G | 40S ribosomal protein S6  
H | 40S ribosomal protein S7  
I | 40S ribosomal protein S8  
J | KLLA0E23673p  
K | KLLA0B08173p  
L | KLLA0A10483p  
N | KLLA0F18040p  
O | 40S ribosomal protein S14  
P | KLLA0F07843p  
Q | 40S ribosomal protein S16  
R | KLLA0B01474p  
S | KLLA0B01562p  
U | KLLA0F25542p  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S22  
X | KLLA0B11231p  
Y | 40S ribosomal protein S24  
a | 40S ribosomal protein S26  
b | 40S ribosomal protein S27  
c | 40S ribosomal protein S28  
d | 40S ribosomal protein S29  
e | 40S ribosomal protein S30  
f | Ubiquitin-40S ribosomal protein S27a  
h | 60S ribosomal protein L41-A  
i | Eukaryotic translation initiation factor 1A  
j | Eukaryotic translation initiation factor 2 subunit alpha  
l | Eukaryotic translation initiation factor 2 subunit beta  
m | Eukaryotic translation initiation factor eIF-1  
p | Eukaryotic translation initiation factor 3 subunit B  
q | Eukaryotic translation initiation factor 3 subunit C  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_2.mrc

Opened 0057_6gsm_2.mrc as #2, grid size 88,144,112, pixel 1, shown at level
0.15, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_2.cif (#1) to map 0057_6gsm_2.mrc (#2) using 40820
atoms  
average map value = 0.08348, steps = 44  
shifted from previous position = 0.372  
rotated from previous position = 0.0986 degrees  
atoms outside contour = 39641, contour level = 0.15035  
  
Position of 0057_6gsm_2.cif (#1) relative to 0057_6gsm_2.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999880 0.00144453 -0.00056816 -0.47396073  
-0.00144411 0.99999868 0.00074240 -0.07299325  
0.00056923 -0.00074158 0.99999956 -0.08745279  
Axis -0.43126971 -0.33054626 -0.83949128  
Axis point 18.35108092 237.97475998 0.00000000  
Rotation angle (degrees) 0.09857567  
Shift along axis 0.30194841  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_2_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 167,133,213,278,236,308

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 18875 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_B.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_B.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_B.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_B.cif  
---  
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 50029  
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
50030  
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
50031  
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
50032  
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
50033  
83 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 50286  
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 50287  
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 50288  
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 50289  
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 50290  
123 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /1:20  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /1:20  
Atom N3 has no neighbors to form bonds with according to residue template for
A /1:54  
Atom O2' has no neighbors to form bonds with according to residue template for
U /1:55  
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:61  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:618  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:626  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:863  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:863  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1034  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1107  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1116  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1120  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1140  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1143  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1143  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1294  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1294  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1295  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1315  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1321  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1614  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1779  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1779  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1780  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1780  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1781  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /A:76  
Atom N has no neighbors to form bonds with according to residue template for
PHE /A:107  
Atom N has no neighbors to form bonds with according to residue template for
LYS /A:167  
Atom O has no neighbors to form bonds with according to residue template for
PHE /F:50  
Atom O has no neighbors to form bonds with according to residue template for
TYR /F:79  
Atom N has no neighbors to form bonds with according to residue template for
ILE /F:201  
Atom N has no neighbors to form bonds with according to residue template for
SER /N:13  
Atom O has no neighbors to form bonds with according to residue template for
SER /N:13  
Atom O has no neighbors to form bonds with according to residue template for
LYS /N:94  
Atom N has no neighbors to form bonds with according to residue template for
ASP /Q:113  
Atom CB has no neighbors to form bonds with according to residue template for
ASP /Q:113  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /R:14  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /V:69  
Atom N has no neighbors to form bonds with according to residue template for
ASN /V:70  
Atom N has no neighbors to form bonds with according to residue template for
ARG /W:23  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /W:23  
Atom N has no neighbors to form bonds with according to residue template for
HIS /b:31  
Atom O has no neighbors to form bonds with according to residue template for
HIS /b:31  
Atom N has no neighbors to form bonds with according to residue template for
ASP /b:34  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /j:27  
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:56  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /j:63  
Atom N has no neighbors to form bonds with according to residue template for
LEU /j:112  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /j:112  
Atom O has no neighbors to form bonds with according to residue template for
TYR /j:127  
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:158  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /j:158  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /j:229  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /j:229  
Atom O has no neighbors to form bonds with according to residue template for
ILE /m:68  
Atom N has no neighbors to form bonds with according to residue template for
UNK /o:768  
Atom C has no neighbors to form bonds with according to residue template for
UNK /o:768  
Atom N has no neighbors to form bonds with according to residue template for
THR /p:159  
Atom N has no neighbors to form bonds with according to residue template for
ASP /q:333  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /q:348  
Atom N has no neighbors to form bonds with according to residue template for
SER /q:359  
Atom OG has no neighbors to form bonds with according to residue template for
SER /q:359  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /q:366  
Atom CB has no neighbors to form bonds with according to residue template for
ASP /q:400  
Atom N has no neighbors to form bonds with according to residue template for
ASN /q:406  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /q:410  
Atom O has no neighbors to form bonds with according to residue template for
GLN /q:529  
Atom N has no neighbors to form bonds with according to residue template for
LEU /q:550  
Atom CB has no neighbors to form bonds with according to residue template for
LEU /q:550  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /q:550  
Atom C has no neighbors to form bonds with according to residue template for
HIS /q:575  
Atom CD2 has no neighbors to form bonds with according to residue template for
HIS /q:575  
  
Chain information for 0057_6gsm_B.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
A | 40S ribosomal protein S0  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
F | KLLA0D10659p  
N | KLLA0F18040p  
O | 40S ribosomal protein S14  
Q | 40S ribosomal protein S16  
R | KLLA0B01474p  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S22  
a | 40S ribosomal protein S26  
b | 40S ribosomal protein S27  
c | 40S ribosomal protein S28  
h | 60S ribosomal protein L41-A  
j | Eukaryotic translation initiation factor 2 subunit alpha  
m | Eukaryotic translation initiation factor eIF-1  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a  
p | Eukaryotic translation initiation factor 3 subunit B  
q | Eukaryotic translation initiation factor 3 subunit C  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_B.mrc

Opened 0057_6gsm_B.mrc as #2, grid size 112,104,96, pixel 1, shown at level
0.133, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_B.cif (#1) to map 0057_6gsm_B.mrc (#2) using 18875
atoms  
average map value = 0.06864, steps = 56  
shifted from previous position = 0.533  
rotated from previous position = 0.172 degrees  
atoms outside contour = 17837, contour level = 0.13281  
  
Position of 0057_6gsm_B.cif (#1) relative to 0057_6gsm_B.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999713 0.00094651 -0.00220125 0.08733287  
-0.00095051 0.99999790 -0.00181705 0.52019808  
0.00219953 0.00181914 0.99999593 -1.25779506  
Axis 0.60446089 -0.73156077 -0.31535040  
Axis point 562.00964176 0.00000000 20.02717774  
Rotation angle (degrees) 0.17233460  
Shift along axis 0.06887898  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_B_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 173,143,197,252,238,284

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 18871 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_a.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_a.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_a.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_a.cif  
---  
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 50190  
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
50191  
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
50192  
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
50193  
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
50194  
76 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 50447  
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 50448  
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 50449  
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 50450  
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 50451  
141 messages similar to the above omitted  
Atom N4 has no neighbors to form bonds with according to residue template for
C /1:34  
Atom C5 has no neighbors to form bonds with according to residue template for
C /1:34  
Atom O2' has no neighbors to form bonds with according to residue template for
7MG /1:46  
Atom C5' has no neighbors to form bonds with according to residue template for
A /1:59  
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:4  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:10  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:18  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:604  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:604  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:866  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:866  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:867  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:867  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:868  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:868  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:967  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:967  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:972  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1097  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1097  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1118  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1133  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1166  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1166  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1284  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1323  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1325  
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:1330  
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:1410  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1578  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1607  
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:1607  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1643  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1648  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1652  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1652  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1652  
Atom C2' has no neighbors to form bonds with according to residue template for
G /2:1746  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1755  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /A:41  
Atom O4 has no neighbors to form bonds with according to residue template for
U /3:30  
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /B:131  
Atom N has no neighbors to form bonds with according to residue template for
ASN /B:178  
Atom O has no neighbors to form bonds with according to residue template for
ASN /B:178  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /B:178  
Atom N has no neighbors to form bonds with according to residue template for
ASP /B:224  
Atom N has no neighbors to form bonds with according to residue template for
THR /C:122  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /C:135  
Atom N has no neighbors to form bonds with according to residue template for
LEU /C:174  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /C:210  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /F:102  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /F:139  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /F:140  
Atom OG has no neighbors to form bonds with according to residue template for
SER /F:142  
Atom O has no neighbors to form bonds with according to residue template for
TYR /F:211  
Atom N has no neighbors to form bonds with according to residue template for
LYS /Q:14  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /Q:14  
Atom CE has no neighbors to form bonds with according to residue template for
LYS /Q:14  
Atom O has no neighbors to form bonds with according to residue template for
TYR /V:85  
Atom OG has no neighbors to form bonds with according to residue template for
SER /V:86  
Atom N has no neighbors to form bonds with according to residue template for
GLN /W:24  
Atom O has no neighbors to form bonds with according to residue template for
GLN /W:24  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /X:3  
Atom CG has no neighbors to form bonds with according to residue template for
GLU /X:26  
Atom N has no neighbors to form bonds with according to residue template for
LEU /b:7  
Atom N has no neighbors to form bonds with according to residue template for
GLY /j:81  
Atom N has no neighbors to form bonds with according to residue template for
SER /j:105  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /j:107  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /j:107  
Atom N has no neighbors to form bonds with according to residue template for
GLU /j:143  
Atom CB has no neighbors to form bonds with according to residue template for
GLU /j:143  
Atom O has no neighbors to form bonds with according to residue template for
LYS /m:56  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /m:56  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /o:64  
Atom N has no neighbors to form bonds with according to residue template for
ILE /o:97  
Atom N has no neighbors to form bonds with according to residue template for
ARG /o:170  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /o:177  
Atom CD1 has no neighbors to form bonds with according to residue template for
TYR /o:179  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /q:256  
Atom O has no neighbors to form bonds with according to residue template for
ASP /q:305  
Atom O has no neighbors to form bonds with according to residue template for
LYS /q:356  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /q:356  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /q:356  
Atom N has no neighbors to form bonds with according to residue template for
GLU /q:600  
  
Chain information for 0057_6gsm_a.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
A | 40S ribosomal protein S0  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
F | KLLA0D10659p  
N | KLLA0F18040p  
O | 40S ribosomal protein S14  
Q | 40S ribosomal protein S16  
R | KLLA0B01474p  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S22  
X | KLLA0B11231p  
a | 40S ribosomal protein S26  
b | 40S ribosomal protein S27  
c | 40S ribosomal protein S28  
h | 60S ribosomal protein L41-A  
j | Eukaryotic translation initiation factor 2 subunit alpha  
l | Eukaryotic translation initiation factor 2 subunit beta  
m | Eukaryotic translation initiation factor eIF-1  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a  
p | Eukaryotic translation initiation factor 3 subunit B  
q | Eukaryotic translation initiation factor 3 subunit C  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_a.mrc

Opened 0057_6gsm_a.mrc as #2, grid size 80,96,88, pixel 1, shown at level
0.149, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_a.cif (#1) to map 0057_6gsm_a.mrc (#2) using 18871
atoms  
average map value = 0.0811, steps = 56  
shifted from previous position = 0.485  
rotated from previous position = 0.143 degrees  
atoms outside contour = 18299, contour level = 0.14928  
  
Position of 0057_6gsm_a.cif (#1) relative to 0057_6gsm_a.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999911 0.00018452 -0.00132388 0.02105214  
-0.00018729 0.99999778 -0.00209751 0.38372358  
0.00132349 0.00209776 0.99999692 -1.07470455  
Axis 0.84333037 -0.53217264 -0.07474067  
Axis point 0.00000000 516.31993276 155.46967396  
Rotation angle (degrees) 0.14251334  
Shift along axis -0.10612915  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_a_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  


[deleted to fit within ticket limits]

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 118,200,179,205,279,266

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 11207 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_V.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_V.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_V.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_V.cif  
---  
warnings | Invalid residue range for struct_conf "HELX32": invalid chain "I",
near line 42239  
Invalid residue range for struct_conf "HELX33": invalid chain "I", near line
42240  
Invalid residue range for struct_conf "HELX34": invalid chain "I", near line
42241  
Invalid residue range for struct_conf "HELX35": invalid chain "I", near line
42242  
Invalid residue range for struct_conf "HELX36": invalid chain "I", near line
42243  
155 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 47": invalid chain "I", near
line 42507  
Invalid sheet range for struct_sheet_range "? 48": invalid chain "I", near
line 42508  
Invalid sheet range for struct_sheet_range "? 49": invalid chain "J", near
line 42509  
Invalid sheet range for struct_sheet_range "? 50": invalid chain "J", near
line 42510  
Invalid sheet range for struct_sheet_range "? 51": invalid chain "J", near
line 42511  
179 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:11  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:604  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:604  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:604  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:606  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:612  
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:613  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:613  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:633  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:633  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:657  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:679  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:680  
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:696  
Atom C3' has no neighbors to form bonds with according to residue template for
C /2:696  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:751  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:752  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:759  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:788  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:789  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:793  
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:793  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:865  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:865  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:868  
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:868  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:932  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:932  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:961  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:961  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:962  
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:1050  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1053  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1063  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1074  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1075  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1141  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1145  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1626  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1626  
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:1794  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /A:88  
Atom N has no neighbors to form bonds with according to residue template for
GLY /A:100  
Atom CE has no neighbors to form bonds with according to residue template for
LYS /B:145  
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /C:99  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /D:128  
Atom CA has no neighbors to form bonds with according to residue template for
GLU /H:17  
Atom CG has no neighbors to form bonds with according to residue template for
GLU /H:17  
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /H:160  
Atom N has no neighbors to form bonds with according to residue template for
LEU /J:24  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /N:9  
Atom N has no neighbors to form bonds with according to residue template for
SER /R:96  
Atom OG has no neighbors to form bonds with according to residue template for
SER /R:96  
Atom N has no neighbors to form bonds with according to residue template for
LYS /b:70  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /b:70  
  
Chain information for 0057_6gsm_V.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
A | 40S ribosomal protein S0  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
D | KLLA0D08305p  
E | 40S ribosomal protein S4  
H | 40S ribosomal protein S7  
J | KLLA0E23673p  
N | KLLA0F18040p  
R | KLLA0B01474p  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S22  
X | KLLA0B11231p  
a | 40S ribosomal protein S26  
b | 40S ribosomal protein S27  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_V.mrc

Opened 0057_6gsm_V.mrc as #2, grid size 88,80,88, pixel 1, shown at level
0.136, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_V.cif (#1) to map 0057_6gsm_V.mrc (#2) using 11207
atoms  
average map value = 0.07645, steps = 64  
shifted from previous position = 0.297  
rotated from previous position = 0.0534 degrees  
atoms outside contour = 10696, contour level = 0.13618  
  
Position of 0057_6gsm_V.cif (#1) relative to 0057_6gsm_V.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999976 0.00068120 0.00013990 -0.12701812  
-0.00068128 0.99999958 0.00061921 -0.23698402  
-0.00013948 -0.00061930 0.99999980 -0.01443814  
Axis -0.66502858 0.15001438 -0.73159598  
Axis point -361.02664137 128.26419762 0.00000000  
Rotation angle (degrees) 0.05335215  
Shift along axis 0.05948255  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_V_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 118,164,179,205,251,282

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 14494 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_A.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_A.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_A.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_A.cif  
---  
warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
near line 45546  
Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
45547  
Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
45548  
Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
45549  
Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
45550  
84 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
line 45804  
Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
line 45805  
Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
line 45806  
Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
line 45807  
Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
line 45808  
149 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:11  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:371  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:604  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:604  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:604  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:606  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:612  
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:613  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:613  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:633  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:633  
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:635  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:635  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:865  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:865  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:868  
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:868  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:870  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:932  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:932  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:961  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:961  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1074  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1075  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1141  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1151  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1160  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1191  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1196  
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1334  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1381  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1410  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1410  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1411  
Atom C3' has no neighbors to form bonds with according to residue template for
G /2:1414  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1426  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1794  
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:1794  
Atom CB has no neighbors to form bonds with according to residue template for
ASP /B:78  
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /B:78  
Atom O has no neighbors to form bonds with according to residue template for
LYS /B:195  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /D:126  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /D:128  
Atom N has no neighbors to form bonds with according to residue template for
GLU /D:169  
Atom O has no neighbors to form bonds with according to residue template for
GLU /D:169  
Atom CB has no neighbors to form bonds with according to residue template for
GLU /H:134  
Atom N has no neighbors to form bonds with according to residue template for
GLN /H:160  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /H:182  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /H:182  
Atom N has no neighbors to form bonds with according to residue template for
LEU /J:24  
Atom N has no neighbors to form bonds with according to residue template for
VAL /J:101  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /N:9  
Atom C has no neighbors to form bonds with according to residue template for
GLN /N:36  
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /N:40  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /N:40  
Atom N has no neighbors to form bonds with according to residue template for
THR /U:70  
Atom N has no neighbors to form bonds with according to residue template for
ASN /V:3  
Atom CB has no neighbors to form bonds with according to residue template for
ASN /V:3  
Atom N has no neighbors to form bonds with according to residue template for
GLN /W:98  
Atom N has no neighbors to form bonds with according to residue template for
TYR /a:62  
Atom O has no neighbors to form bonds with according to residue template for
TYR /a:62  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /b:52  
Atom O has no neighbors to form bonds with according to residue template for
THR /b:55  
Atom C has no neighbors to form bonds with according to residue template for
VAL /b:62  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /c:13  
Atom O has no neighbors to form bonds with according to residue template for
ARG /c:64  
Atom O has no neighbors to form bonds with according to residue template for
GLN /g:70  
Atom N has no neighbors to form bonds with according to residue template for
ASP /g:87  
Atom C has no neighbors to form bonds with according to residue template for
ASP /g:87  
Atom NE1 has no neighbors to form bonds with according to residue template for
TRP /g:135  
Atom CZ2 has no neighbors to form bonds with according to residue template for
TRP /g:135  
Atom O has no neighbors to form bonds with according to residue template for
PRO /g:283  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /o:10  
Atom N has no neighbors to form bonds with according to residue template for
LEU /o:56  
Atom N has no neighbors to form bonds with according to residue template for
LYS /o:95  
Atom O has no neighbors to form bonds with according to residue template for
GLU /o:204  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /o:204  
Atom O has no neighbors to form bonds with according to residue template for
ASP /o:262  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /o:262  
Atom N has no neighbors to form bonds with according to residue template for
ASP /q:599  
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /q:599  
  
Chain information for 0057_6gsm_A.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
A | 40S ribosomal protein S0  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
D | KLLA0D08305p  
H | 40S ribosomal protein S7  
J | KLLA0E23673p  
N | KLLA0F18040p  
Q | 40S ribosomal protein S16  
R | KLLA0B01474p  
U | KLLA0F25542p  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S22  
X | KLLA0B11231p  
a | 40S ribosomal protein S26  
b | 40S ribosomal protein S27  
c | 40S ribosomal protein S28  
d | 40S ribosomal protein S29  
g | KLLA0E12277p  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a  
q | Eukaryotic translation initiation factor 3 subunit C  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_A.mrc

Opened 0057_6gsm_A.mrc as #2, grid size 88,88,104, pixel 1, shown at level
0.131, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_A.cif (#1) to map 0057_6gsm_A.mrc (#2) using 14494
atoms  
average map value = 0.07084, steps = 76  
shifted from previous position = 0.352  
rotated from previous position = 0.118 degrees  
atoms outside contour = 13791, contour level = 0.13132  
  
Position of 0057_6gsm_A.cif (#1) relative to 0057_6gsm_A.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999821 -0.00143912 0.00122460 0.07260505  
0.00143809 0.99999861 0.00083845 -0.68512420  
-0.00122581 -0.00083669 0.99999890 0.13899326  
Axis -0.40522153 0.59276321 0.69600811  
Axis point 336.72037114 -45.36388925 -0.00000000  
Rotation angle (degrees) 0.11842687  
Shift along axis -0.33879711  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_A_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 99,136,119,226,231,246

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 26755 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_D.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_D.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_D.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_D.cif  
---  
warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
near line 58128  
Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
58129  
Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
58130  
Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
58131  
Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
58132  
113 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
line 58386  
Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
line 58387  
Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
line 58388  
Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
line 58389  
Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
line 58390  
127 messages similar to the above omitted  
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:39  
Atom O2 has no neighbors to form bonds with according to residue template for
C /1:39  
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:40  
Atom O2 has no neighbors to form bonds with according to residue template for
C /1:40  
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:41  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:488  
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:505  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:935  
Atom C2' has no neighbors to form bonds with according to residue template for
G /2:937  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1033  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1033  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1072  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1107  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1107  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1179  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1182  
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1182  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1228  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1228  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1252  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1350  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1371  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1469  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1469  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1503  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1506  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1506  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1508  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1538  
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:1539  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1561  
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:1561  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1771  
Atom N has no neighbors to form bonds with according to residue template for
SER /A:2  
Atom N has no neighbors to form bonds with according to residue template for
THR /A:10  
Atom C has no neighbors to form bonds with according to residue template for
GLU /A:12  
Atom N has no neighbors to form bonds with according to residue template for
LYS /A:27  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /A:27  
Atom N has no neighbors to form bonds with according to residue template for
VAL /A:37  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /A:37  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /3:30  
Atom O5' has no neighbors to form bonds with according to residue template for
U /3:30  
Atom N has no neighbors to form bonds with according to residue template for
LEU /C:63  
Atom ND1 has no neighbors to form bonds with according to residue template for
HIS /C:115  
Atom N has no neighbors to form bonds with according to residue template for
SER /C:171  
Atom OG has no neighbors to form bonds with according to residue template for
SER /C:171  
Atom N has no neighbors to form bonds with according to residue template for
LYS /F:111  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /F:111  
Atom N has no neighbors to form bonds with according to residue template for
THR /F:209  
Atom N has no neighbors to form bonds with according to residue template for
ASP /M:32  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /M:104  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /M:105  
Atom N has no neighbors to form bonds with according to residue template for
ALA /O:59  
Atom C has no neighbors to form bonds with according to residue template for
ALA /O:59  
Atom N has no neighbors to form bonds with according to residue template for
ALA /O:64  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /O:64  
Atom N has no neighbors to form bonds with according to residue template for
GLN /O:65  
Atom O has no neighbors to form bonds with according to residue template for
ARG /O:132  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /O:132  
Atom O has no neighbors to form bonds with according to residue template for
ARG /O:135  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /O:135  
Atom N has no neighbors to form bonds with according to residue template for
SER /P:66  
Atom O has no neighbors to form bonds with according to residue template for
SER /P:92  
Atom O has no neighbors to form bonds with according to residue template for
ASN /P:103  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /P:112  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /Q:3  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /Q:3  
Atom N has no neighbors to form bonds with according to residue template for
HIS /Q:21  
Atom O has no neighbors to form bonds with according to residue template for
LYS /Q:47  
Atom C has no neighbors to form bonds with according to residue template for
GLU /Q:50  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /S:131  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /T:84  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /T:84  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /V:49  
Atom N has no neighbors to form bonds with according to residue template for
LEU /V:72  
Atom C has no neighbors to form bonds with according to residue template for
LEU /V:72  
Atom N has no neighbors to form bonds with according to residue template for
GLN /V:74  
Atom N has no neighbors to form bonds with according to residue template for
SER /V:84  
Atom O has no neighbors to form bonds with according to residue template for
SER /X:66  
Atom O has no neighbors to form bonds with according to residue template for
LYS /X:112  
Atom O has no neighbors to form bonds with according to residue template for
TRP /X:136  
Atom N has no neighbors to form bonds with according to residue template for
ASN /a:43  
Atom O has no neighbors to form bonds with according to residue template for
ASN /a:43  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /a:51  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /c:38  
Atom O has no neighbors to form bonds with according to residue template for
ASN /e:46  
Atom O has no neighbors to form bonds with according to residue template for
LYS /i:64  
Atom CE1 has no neighbors to form bonds with according to residue template for
TYR /j:13  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /j:13  
Atom N has no neighbors to form bonds with according to residue template for
LEU /j:51  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /j:51  
Atom N has no neighbors to form bonds with according to residue template for
LEU /j:85  
Atom O has no neighbors to form bonds with according to residue template for
LEU /j:85  
  
Chain information for 0057_6gsm_D.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
A | 40S ribosomal protein S0  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
D | KLLA0D08305p  
F | KLLA0D10659p  
K | KLLA0B08173p  
M | 40S ribosomal protein S12  
N | KLLA0F18040p  
O | 40S ribosomal protein S14  
P | KLLA0F07843p  
Q | 40S ribosomal protein S16  
R | KLLA0B01474p  
S | KLLA0B01562p  
T | KLLA0A07194p  
U | KLLA0F25542p  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S22  
X | KLLA0B11231p  
a | 40S ribosomal protein S26  
b | 40S ribosomal protein S27  
c | 40S ribosomal protein S28  
d | 40S ribosomal protein S29  
e | 40S ribosomal protein S30  
f | Ubiquitin-40S ribosomal protein S27a  
g | KLLA0E12277p  
i | Eukaryotic translation initiation factor 1A  
j | Eukaryotic translation initiation factor 2 subunit alpha  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_D.mrc

Opened 0057_6gsm_D.mrc as #2, grid size 128,96,128, pixel 1, shown at level
0.13, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_D.cif (#1) to map 0057_6gsm_D.mrc (#2) using 26755
atoms  
average map value = 0.07567, steps = 60  
shifted from previous position = 0.287  
rotated from previous position = 0.0358 degrees  
atoms outside contour = 25381, contour level = 0.13032  
  
Position of 0057_6gsm_D.cif (#1) relative to 0057_6gsm_D.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999997 0.00024737 -0.00006156 -0.14997849  
-0.00024741 0.99999981 -0.00057026 -0.03289269  
0.00006142 0.00057028 0.99999984 -0.29491317  
Axis 0.91294090 -0.09843458 -0.39604236  
Axis point 0.00000000 528.85055684 -60.77398035  
Rotation angle (degrees) 0.03578978  
Shift along axis -0.01688561  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_D_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 163,198,217,258,285,304

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 16843 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_N.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_N.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_N.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_N.cif  
---  
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 48034  
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
48035  
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
48036  
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
48037  
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
48038  
91 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 48291  
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 48292  
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 48293  
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 48294  
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 48295  
137 messages similar to the above omitted  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:111  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:302  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:334  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:610  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:610  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:648  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:682  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:682  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:682  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:847  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:847  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:850  
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:850  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:851  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:851  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:851  
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:851  
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:929  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:929  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:930  
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:993  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1084  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1087  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1106  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1129  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1627  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1764  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1764  
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:1764  
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1777  
Atom N3 has no neighbors to form bonds with according to residue template for
C /2:1781  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1781  
Atom N has no neighbors to form bonds with according to residue template for
VAL /A:50  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /A:50  
Atom N has no neighbors to form bonds with according to residue template for
THR /A:80  
Atom C has no neighbors to form bonds with according to residue template for
THR /A:80  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /A:101  
Atom CB has no neighbors to form bonds with according to residue template for
PRO /A:118  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /A:135  
Atom CD2 has no neighbors to form bonds with according to residue template for
HIS /A:168  
Atom NE1 has no neighbors to form bonds with according to residue template for
TRP /A:174  
Atom CZ2 has no neighbors to form bonds with according to residue template for
TRP /A:174  
Atom O has no neighbors to form bonds with according to residue template for
PRO /C:232  
Atom CD has no neighbors to form bonds with according to residue template for
ARG /H:88  
Atom N has no neighbors to form bonds with according to residue template for
THR /L:6  
Atom O has no neighbors to form bonds with according to residue template for
LYS /L:57  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /L:67  
Atom N has no neighbors to form bonds with according to residue template for
VAL /L:94  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /L:94  
Atom O has no neighbors to form bonds with according to residue template for
TYR /L:97  
Atom CB has no neighbors to form bonds with according to residue template for
TYR /L:97  
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /V:23  
Atom N has no neighbors to form bonds with according to residue template for
ILE /V:24  
Atom N has no neighbors to form bonds with according to residue template for
GLN /V:74  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /V:81  
Atom N has no neighbors to form bonds with according to residue template for
HIS /W:117  
Atom C has no neighbors to form bonds with according to residue template for
HIS /W:117  
Atom N has no neighbors to form bonds with according to residue template for
ARG /X:16  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /X:16  
Atom N has no neighbors to form bonds with according to residue template for
LYS /h:16  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /h:16  
Atom N has no neighbors to form bonds with according to residue template for
SER /p:89  
Atom OG has no neighbors to form bonds with according to residue template for
SER /p:89  
Atom N has no neighbors to form bonds with according to residue template for
LEU /q:329  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /q:408  
Atom N has no neighbors to form bonds with according to residue template for
ILE /q:503  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /q:546  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /q:546  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /q:566  
Atom O has no neighbors to form bonds with according to residue template for
LEU /q:567  
Atom C has no neighbors to form bonds with according to residue template for
THR /q:670  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /q:670  
Atom N has no neighbors to form bonds with according to residue template for
ARG /q:672  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /q:672  
  
Chain information for 0057_6gsm_N.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
A | 40S ribosomal protein S0  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
E | 40S ribosomal protein S4  
H | 40S ribosomal protein S7  
I | 40S ribosomal protein S8  
L | KLLA0A10483p  
N | KLLA0F18040p  
O | 40S ribosomal protein S14  
R | KLLA0B01474p  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S22  
X | KLLA0B11231p  
a | 40S ribosomal protein S26  
b | 40S ribosomal protein S27  
h | 60S ribosomal protein L41-A  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a  
p | Eukaryotic translation initiation factor 3 subunit B  
q | Eukaryotic translation initiation factor 3 subunit C  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_N.mrc

Opened 0057_6gsm_N.mrc as #2, grid size 96,88,88, pixel 1, shown at level
0.146, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_N.cif (#1) to map 0057_6gsm_N.mrc (#2) using 16843
atoms  
average map value = 0.07727, steps = 56  
shifted from previous position = 0.537  
rotated from previous position = 0.0952 degrees  
atoms outside contour = 16191, contour level = 0.14631  
  
Position of 0057_6gsm_N.cif (#1) relative to 0057_6gsm_N.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999868 0.00059240 -0.00150967 -0.02680054  
-0.00059186 0.99999976 0.00036035 -0.23872813  
0.00150989 -0.00035945 0.99999880 -0.60628094  
Axis -0.21665054 -0.90884921 -0.35644867  
Axis point 297.96676729 0.00000000 44.97111143  
Rotation angle (degrees) 0.09517979  
Shift along axis 0.43888226  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_N_fitted.cif #1

> close #1

> close #2

> open 6gsm

6gsm title:  
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]  
  
Chain information for 6gsm #1  
---  
Chain | Description | UniProt  
1 | Met-tRNAi |  
2 | 18S ribosomal RNA |  
3 | mRNA (5'-R(P*AP*AP*U)-3') |  
A | 40S ribosomal protein S0 | RSSA_KLULA 2-209  
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233  
C | KLLA0F09812p | Q6CKL3_KLULA 39-255  
D | KLLA0D08305p | Q6CRK7_KLULA 3-225  
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261  
F | KLLA0D10659p | Q6CRA3_KLULA 22-227  
G | 40S ribosomal protein S6 | RS6_KLULA 1-226  
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187  
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201  
J | KLLA0E23673p | Q6CM18_KLULA 2-183  
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96  
L | KLLA0A10483p | Q6CX80_KLULA 2-156  
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134  
N | KLLA0F18040p | Q6CJK0_KLULA 2-151  
O | 40S ribosomal protein S14 | RS14_KLULA 11-137  
P | KLLA0F07843p | Q6CKV4_KLULA 13-131  
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143  
R | KLLA0B01474p | Q6CWU3_KLULA 2-126  
S | KLLA0B01562p | Q6CWT9_KLULA 2-146  
T | KLLA0A07194p | Q6CXM0_KLULA 2-144  
U | KLLA0F25542p | Q6CIM1_KLULA 15-120  
V | 40S ribosomal protein S21 | RS21_KLULA 1-87  
W | 40S ribosomal protein S22 | RS22_KLULA 2-130  
X | KLLA0B11231p | F2Z602_KLULA 2-145  
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135  
Z | KLLA0B06182p | Q6CW78_KLULA 36-105  
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99  
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82  
c | 40S ribosomal protein S28 | RS28_KLULA 6-67  
d | 40S ribosomal protein S29 | RS29_KLULA 4-56  
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61  
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150  
g | KLLA0E12277p | Q6CNI7_KLULA 3-326  
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25  
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115  
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265  
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519  
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270  
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492  
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737  
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794  
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96  
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342  
  
Non-standard residues in 6gsm #1  
---  
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate  
GCP — phosphomethylphosphonic acid guanylate ester  
MG — magnesium ion  
ZN — zinc ion  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc

Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
level 0.0673, step 2, values float32  

> volume #2 region 190,134,203,261,229,290

> open /scratch/cs-bioinfo/tngu/6k_data/select_box.py

FYI: command is replacing existing command: "selectbox"  
executed select_box.py  

> selectbox #1 inMap #2

Selected 14545 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_O.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_O.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_O.cif


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.5 (Core Profile) Mesa 22.3.0
OpenGL renderer: llvmpipe (LLVM 15.0.0, 256 bits)
OpenGL vendor: Mesa/X.org

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=wahab-01:1006.0
Manufacturer: Dell Inc.
Model: PowerEdge C6420
OS: Rocky Linux 8.8 Green Obsidian
Architecture: 64bit 
Virtual Machine: none
CPU: 40 Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Cache Size: 28160 KB
Memory:
	MemTotal:       394830928 kB
	MemFree:        224418136 kB
	MemAvailable:   389593440 kB

Graphics:
	unknown

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.0
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    torch: 1.13.1+cu117
    torchaudio: 0.13.1+cu117
    torchvision: 0.14.1+cu117
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by pett, 2 years ago

Component:	Unassigned → Input/Output
Description:	modified (diff)
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Crash opening mmCIF file

Reported by Thu Nguyen

comment:2 by Greg Couch, 6 months ago

Resolution:	→ duplicate
Status:	assigned → closed

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