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Opened 2 years ago

Last modified 6 months ago

#9621 closed defect

ChimeraX bug report submission — at Initial Version

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

Description

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  
  

> 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 115,125,134,226,196,205

> 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 13328 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 44477  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
44478  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
44479  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
44480  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
44481  
174 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
44730  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
44731  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
44732  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
44733  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
44734  
181 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 C8 has no neighbors to form bonds with according to residue template for
A /2:1159  
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 OP2 has no neighbors to form bonds with according to residue template for
G /2:1262  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1313  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1386  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1477  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1581  
Atom N3 has no neighbors to form bonds with according to residue template for
A /3:28  
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 OE1 has no neighbors to form bonds with according to residue template for
GLN /D:101  
Atom O has no neighbors to form bonds with according to residue template for
ALA /D:147  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /F:76  
Atom SD has no neighbors to form bonds with according to residue template for
MET /F:101  
Atom O has no neighbors to form bonds with according to residue template for
TYR /K:12  
Atom CD1 has no neighbors to form bonds with according to residue template for
PHE /K:16  
Atom N has no neighbors to form bonds with according to residue template for
VAL /K:74  
Atom N has no neighbors to form bonds with according to residue template for
LYS /P:24  
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 N has no neighbors to form bonds with according to residue template for
LYS /Q:26  
Atom C has no neighbors to form bonds with according to residue template for
LYS /Q:26  
Atom N has no neighbors to form bonds with according to residue template for
TYR /Q:92  
Atom O has no neighbors to form bonds with according to residue template for
LYS /R:32  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /R:32  
Atom O has no neighbors to form bonds with according to residue template for
ARG /R:33  
Atom O has no neighbors to form bonds with according to residue template for
TRP /S:84  
Atom N has no neighbors to form bonds with according to residue template for
ASN /S:93  
Atom N has no neighbors to form bonds with according to residue template for
LEU /S:113  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /S:131  
Atom O has no neighbors to form bonds with according to residue template for
LEU /T:45  
Atom N has no neighbors to form bonds with according to residue template for
ARG /f:92  
Atom N has no neighbors to form bonds with according to residue template for
TRP /g:93  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /g:124  
Atom O has no neighbors to form bonds with according to residue template for
ASP /g:150  
Atom O has no neighbors to form bonds with according to residue template for
ILE /g:195  
  
Chain information for 0057_6gsm_U.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
C | KLLA0F09812p  
D | KLLA0D08305p  
F | KLLA0D10659p  
K | KLLA0B08173p  
P | KLLA0F07843p  
Q | 40S ribosomal protein S16  
R | KLLA0B01474p  
S | KLLA0B01562p  
T | KLLA0A07194p  
U | KLLA0F25542p  
Z | KLLA0B06182p  
d | 40S ribosomal protein S29  
f | Ubiquitin-40S ribosomal protein S27a  
g | KLLA0E12277p  
i | Eukaryotic translation initiation factor 1A  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U.mrc

Opened 0057_6gsm_U.mrc as #2, grid size 112,72,72, pixel 1, shown at level
0.134, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_U.cif (#1) to map 0057_6gsm_U.mrc (#2) using 13328
atoms  
average map value = 0.07934, steps = 48  
shifted from previous position = 0.338  
rotated from previous position = 0.177 degrees  
atoms outside contour = 12826, contour level = 0.13392  
  
Position of 0057_6gsm_U.cif (#1) relative to 0057_6gsm_U.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999647 0.00033916 0.00263397 -0.67215769  
-0.00034329 0.99999871 0.00156937 -0.49700188  
-0.00263344 -0.00157026 0.99999530 0.68166280  
Axis -0.50885627 0.85371602 -0.11060857  
Axis point 251.71663719 0.00000000 285.98413263  
Rotation angle (degrees) 0.17675705  
Shift along axis -0.15766456  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U_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 162,185,127,257,272,198

> 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 11728 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 42816  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
42817  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
42818  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
42819  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
42820  
163 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
43069  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
43070  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
43071  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
43072  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
43073  
166 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:18  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:97  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:359  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:389  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:411  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:411  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:421  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:425  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:532  
Atom C3' has no neighbors to form bonds with according to residue template for
A /2:533  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:757  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:765  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:767  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1132  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1256  
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:1257  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1259  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1266  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1289  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1291  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1299  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1299  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1325  
Atom N7 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
A /2:1631  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1659  
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1743  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1745  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1745  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1750  
Atom N has no neighbors to form bonds with according to residue template for
HIS /C:115  
Atom CB 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
GLY /C:117  
Atom CA has no neighbors to form bonds with according to residue template for
ILE /C:120  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /C:120  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /C:120  
Atom CB has no neighbors to form bonds with according to residue template for
PRO /C:178  
Atom N has no neighbors to form bonds with according to residue template for
VAL /C:201  
Atom O has no neighbors to form bonds with according to residue template for
VAL /C:201  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /C:209  
Atom O has no neighbors to form bonds with according to residue template for
GLY /D:36  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /D:50  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /D:62  
Atom CG has no neighbors to form bonds with according to residue template for
GLN /J:139  
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /J:139  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /J:151  
Atom O has no neighbors to form bonds with according to residue template for
GLU /J:183  
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /K:12  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /K:12  
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /K:47  
Atom N has no neighbors to form bonds with according to residue template for
GLN /K:58  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /l:216  
Atom N has no neighbors to form bonds with according to residue template for
SER /l:219  
Atom OG has no neighbors to form bonds with according to residue template for
SER /l:219  
Atom N has no neighbors to form bonds with according to residue template for
GLN /m:31  
Atom C has no neighbors to form bonds with according to residue template for
GLN /m:31  
Atom N has no neighbors to form bonds with according to residue template for
CYS /m:89  
Atom SG has no neighbors to form bonds with according to residue template for
CYS /m:89  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /p:390  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /p:390  
Atom N has no neighbors to form bonds with according to residue template for
GLU /p:398  
Atom O has no neighbors to form bonds with according to residue template for
ASN /p:412  
Atom N has no neighbors to form bonds with according to residue template for
VAL /p:480  
Atom O has no neighbors to form bonds with according to residue template for
VAL /p:480  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /p:530  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /p:530  
  
Chain information for 0057_6gsm_e.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
C | KLLA0F09812p  
D | KLLA0D08305p  
J | KLLA0E23673p  
K | KLLA0B08173p  
M | 40S ribosomal protein S12  
X | KLLA0B11231p  
e | 40S ribosomal protein S30  
i | Eukaryotic translation initiation factor 1A  
l | Eukaryotic translation initiation factor 2 subunit beta  
m | Eukaryotic translation initiation factor eIF-1  
p | Eukaryotic translation initiation factor 3 subunit B  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_e.mrc

Opened 0057_6gsm_e.mrc as #2, grid size 96,88,72, pixel 1, shown at level
0.14, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_e.cif (#1) to map 0057_6gsm_e.mrc (#2) using 11728
atoms  
average map value = 0.07883, steps = 48  
shifted from previous position = 0.345  
rotated from previous position = 0.156 degrees  
atoms outside contour = 11229, contour level = 0.14039  
  
Position of 0057_6gsm_e.cif (#1) relative to 0057_6gsm_e.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999931 -0.00096213 -0.00066854 0.07989544  
0.00096378 0.99999650 0.00246569 -0.83572949  
0.00066616 -0.00246633 0.99999674 0.52309429  
Axis -0.90324313 -0.24443575 0.35270810  
Axis point 0.00000000 166.40782257 307.79255316  
Rotation angle (degrees) 0.15642749  
Shift along axis 0.31661676  
  

> 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 130,174,165,225,277,244

> 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 19056 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C.cif  
---  
warnings | Invalid residue range for struct_conf "HELX41": invalid chain "J",
near line 50359  
Invalid residue range for struct_conf "HELX42": invalid chain "J", near line
50360  
Invalid residue range for struct_conf "HELX43": invalid chain "J", near line
50361  
Invalid residue range for struct_conf "HELX51": invalid chain "L", near line
50369  
Invalid residue range for struct_conf "HELX52": invalid chain "L", near line
50370  
119 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 49": invalid chain "J", near
line 50620  
Invalid sheet range for struct_sheet_range "? 50": invalid chain "J", near
line 50621  
Invalid sheet range for struct_sheet_range "? 51": invalid chain "J", near
line 50622  
Invalid sheet range for struct_sheet_range "? 52": invalid chain "J", near
line 50623  
Invalid sheet range for struct_sheet_range "? 53": invalid chain "J", near
line 50624  
110 messages similar to the above omitted  
Atom O4' has no neighbors to form bonds with according to residue template for
U /1:36  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:28  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:33  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:41  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:107  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:107  
Atom P has no neighbors to form bonds with according to residue template for U
/2:110  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:461  
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:465  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:486  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:486  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:565  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:587  
Atom N3 has no neighbors to form bonds with according to residue template for
U /2:587  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:587  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:600  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:644  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:644  
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:644  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:664  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:664  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:675  
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:675  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:689  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:689  
Atom C3' has no neighbors to form bonds with according to residue template for
A /2:755  
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:756  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:864  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:864  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:942  
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:942  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1024  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1186  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1188  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1191  
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:1191  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1192  
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1311  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1394  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1394  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1417  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1430  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1618  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1638  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1767  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1787  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /A:8  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /3:29  
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 CG2 has no neighbors to form bonds with according to residue template for
ILE /E:248  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /E:248  
Atom CE has no neighbors to form bonds with according to residue template for
LYS /H:105  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /J:113  
Atom N has no neighbors to form bonds with according to residue template for
TYR /J:114  
Atom C has no neighbors to form bonds with according to residue template for
TYR /J:114  
Atom N has no neighbors to form bonds with according to residue template for
LYS /J:138  
Atom CE has no neighbors to form bonds with according to residue template for
LYS /J:138  
Atom O has no neighbors to form bonds with according to residue template for
GLN /J:139  
Atom N has no neighbors to form bonds with according to residue template for
ASN /J:142  
Atom O has no neighbors to form bonds with according to residue template for
LYS /L:105  
Atom N has no neighbors to form bonds with according to residue template for
SER /L:144  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /O:92  
Atom CB has no neighbors to form bonds with according to residue template for
LEU /O:137  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /O:137  
Atom N has no neighbors to form bonds with according to residue template for
GLY /R:2  
Atom N has no neighbors to form bonds with according to residue template for
LYS /R:44  
Atom O has no neighbors to form bonds with according to residue template for
LYS /R:44  
Atom N has no neighbors to form bonds with according to residue template for
SER /X:66  
Atom OG has no neighbors to form bonds with according to residue template for
SER /X:66  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /X:69  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /X:69  
Atom N has no neighbors to form bonds with according to residue template for
SER /a:27  
Atom N has no neighbors to form bonds with according to residue template for
LEU /b:8  
Atom O has no neighbors to form bonds with according to residue template for
ARG /c:67  
Atom N has no neighbors to form bonds with according to residue template for
PHE /d:43  
Atom O has no neighbors to form bonds with according to residue template for
ARG /e:37  
Atom N has no neighbors to form bonds with according to residue template for
THR /g:131  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /g:131  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /g:152  
Atom OG has no neighbors to form bonds with according to residue template for
SER /g:176  
Atom N has no neighbors to form bonds with according to residue template for
ASN /g:207  
Atom N has no neighbors to form bonds with according to residue template for
TRP /g:230  
Atom CE has no neighbors to form bonds with according to residue template for
MET /g:239  
Atom N has no neighbors to form bonds with according to residue template for
VAL /g:247  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /i:23  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /i:23  
Atom O has no neighbors to form bonds with according to residue template for
LYS /i:67  
  
Chain information for 0057_6gsm_C.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  
H | 40S ribosomal protein S7  
J | KLLA0E23673p  
L | KLLA0A10483p  
N | KLLA0F18040p  
O | 40S ribosomal protein S14  
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  
e | 40S ribosomal protein S30  
g | KLLA0E12277p  
i | Eukaryotic translation initiation factor 1A  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C.mrc

Opened 0057_6gsm_C.mrc as #2, grid size 96,104,80, pixel 1, shown at level
0.146, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_C.cif (#1) to map 0057_6gsm_C.mrc (#2) using 19056
atoms  
average map value = 0.0813, steps = 60  
shifted from previous position = 0.29  
rotated from previous position = 0.049 degrees  
atoms outside contour = 18418, contour level = 0.14602  
  
Position of 0057_6gsm_C.cif (#1) relative to 0057_6gsm_C.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00002143 0.00013169 -0.07370813  
0.00002132 0.99999964 0.00084431 -0.39245208  
-0.00013171 -0.00084430 0.99999963 0.02626946  
Axis -0.98774211 0.15407786 0.02501082  
Axis point 0.00000000 30.52682018 467.20587978  
Rotation angle (degrees) 0.04897546  
Shift along axis 0.01299346  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C_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 179,79,129,258,182,224

> 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 13752 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 44865  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
44866  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
44867  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
44868  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
44869  
168 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
45118  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
45119  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
45120  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
45121  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
45122  
203 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /1:6  
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:6  
Atom O3' has no neighbors to form bonds with according to residue template for
U /1:50  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1232  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1258  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1266  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1266  
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:1266  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1286  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1329  
Atom C5 has no neighbors to form bonds with according to residue template for
A /2:1398  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1398  
Atom O3' 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
G /2:1484  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1487  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1489  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1496  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1497  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1508  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1517  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1517  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /F:66  
Atom N has no neighbors to form bonds with according to residue template for
SER /F:67  
Atom C has no neighbors to form bonds with according to residue template for
SER /F:67  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /F:128  
Atom CD1 has no neighbors to form bonds with according to residue template for
TYR /K:12  
Atom N has no neighbors to form bonds with according to residue template for
LEU /K:46  
Atom N has no neighbors to form bonds with according to residue template for
TYR /K:66  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /Q:38  
Atom N has no neighbors to form bonds with according to residue template for
LYS /Q:47  
Atom N has no neighbors to form bonds with according to residue template for
ARG /T:63  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /T:63  
Atom CD has no neighbors to form bonds with according to residue template for
ARG /T:63  
Atom N has no neighbors to form bonds with according to residue template for
THR /c:26  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /c:26  
Atom N has no neighbors to form bonds with according to residue template for
VAL /c:48  
Atom O has no neighbors to form bonds with according to residue template for
VAL /c:48  
Atom N has no neighbors to form bonds with according to residue template for
ASN /d:48  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /d:48  
Atom O has no neighbors to form bonds with according to residue template for
ASN /j:41  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /j:41  
Atom N has no neighbors to form bonds with according to residue template for
ALA /j:71  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /j:71  
Atom O has no neighbors to form bonds with according to residue template for
ARG /j:88  
Atom CA has no neighbors to form bonds with according to residue template for
GLU /j:93  
Atom CG has no neighbors to form bonds with according to residue template for
GLU /j:93  
Atom N has no neighbors to form bonds with according to residue template for
ASP /j:94  
Atom N has no neighbors to form bonds with according to residue template for
ALA /j:116  
Atom C has no neighbors to form bonds with according to residue template for
ALA /j:116  
Atom O has no neighbors to form bonds with according to residue template for
GLN /j:120  
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:173  
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /j:173  
Atom O has no neighbors to form bonds with according to residue template for
VAL /l:225  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /l:225  
Atom CA has no neighbors to form bonds with according to residue template for
LEU /l:226  
Atom O has no neighbors to form bonds with according to residue template for
LEU /l:226  
Atom O has no neighbors to form bonds with according to residue template for
MET /m:74  
  
Chain information for 0057_6gsm_S.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
D | KLLA0D08305p  
F | KLLA0D10659p  
K | KLLA0B08173p  
P | KLLA0F07843p  
Q | 40S ribosomal protein S16  
R | KLLA0B01474p  
S | KLLA0B01562p  
T | KLLA0A07194p  
U | KLLA0F25542p  
Z | KLLA0B06182p  
c | 40S ribosomal protein S28  
d | 40S ribosomal protein S29  
f | Ubiquitin-40S ribosomal protein S27a  
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_S.mrc

Opened 0057_6gsm_S.mrc as #2, grid size 80,104,96, pixel 1, shown at level
0.127, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_S.cif (#1) to map 0057_6gsm_S.mrc (#2) using 13752
atoms  
average map value = 0.07525, steps = 48  
shifted from previous position = 0.41  
rotated from previous position = 0.0854 degrees  
atoms outside contour = 13058, contour level = 0.12703  
  
Position of 0057_6gsm_S.cif (#1) relative to 0057_6gsm_S.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999906 0.00133714 0.00031755 -0.63883129  
-0.00133696 0.99999894 -0.00057716 0.36463028  
-0.00031832 0.00057673 0.99999978 -0.16205439  
Axis 0.38707716 0.21330452 -0.89703537  
Axis point 276.20794680 470.96878257 0.00000000  
Rotation angle (degrees) 0.08540052  
Shift along axis -0.02413119  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S_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 206,188,189,285,251,244

> 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 8610 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 39713  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
39714  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
39715  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
39716  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
39717  
114 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
39966  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
39967  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
39968  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
39969  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
39970  
157 messages similar to the above omitted  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:11  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:20  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:309  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:373  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:605  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:611  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:612  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:613  
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:613  
Atom P has no neighbors to form bonds with according to residue template for G
/2:633  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:942  
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:942  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:997  
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:997  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1000  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1008  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1009  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1018  
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:1018  
Atom O2' 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 /2:1142  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1734  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1794  
Atom C8 has no neighbors to form bonds with according to residue template for
A /3:29  
Atom CA has no neighbors to form bonds with according to residue template for
LYS /N:9  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /O:92  
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
ASN /X:79  
Atom O has no neighbors to form bonds with according to residue template for
ALA /X:113  
Atom C has no neighbors to form bonds with according to residue template for
LEU /i:42  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /i:42  
Atom N has no neighbors to form bonds with according to residue template for
ASN /i:44  
Atom N has no neighbors to form bonds with according to residue template for
GLY /m:107  
Atom O has no neighbors to form bonds with according to residue template for
GLY /m:107  
Atom N has no neighbors to form bonds with according to residue template for
GLY /p:132  
Atom O has no neighbors to form bonds with according to residue template for
GLY /p:132  
Atom O has no neighbors to form bonds with according to residue template for
PRO /p:181  
Atom CB has no neighbors to form bonds with according to residue template for
LEU /p:189  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /p:189  
Atom O has no neighbors to form bonds with according to residue template for
LYS /p:241  
Atom N has no neighbors to form bonds with according to residue template for
ARG /p:266  
Atom N has no neighbors to form bonds with according to residue template for
LEU /p:284  
Atom N has no neighbors to form bonds with according to residue template for
GLU /p:295  
Atom CB has no neighbors to form bonds with according to residue template for
GLU /p:295  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /p:295  
Atom O has no neighbors to form bonds with according to residue template for
GLU /p:308  
Atom CA has no neighbors to form bonds with according to residue template for
ASP /p:397  
Atom O has no neighbors to form bonds with according to residue template for
THR /q:141  
Atom CB has no neighbors to form bonds with according to residue template for
THR /q:141  
Atom O has no neighbors to form bonds with according to residue template for
GLN /q:159  
  
Chain information for 0057_6gsm_h.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
C | KLLA0F09812p  
L | KLLA0A10483p  
N | KLLA0F18040p  
O | 40S ribosomal protein S14  
X | KLLA0B11231p  
a | 40S ribosomal protein S26  
h | 60S ribosomal protein L41-A  
i | Eukaryotic translation initiation factor 1A  
k | Eukaryotic translation initiation factor 2 subunit gamma  
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_h.mrc

Opened 0057_6gsm_h.mrc as #2, grid size 80,64,56, pixel 1, shown at level
0.155, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_h.cif (#1) to map 0057_6gsm_h.mrc (#2) using 8610 atoms  
average map value = 0.08394, steps = 76  
shifted from previous position = 0.502  
rotated from previous position = 0.277 degrees  
atoms outside contour = 8377, contour level = 0.1553  
  
Position of 0057_6gsm_h.cif (#1) relative to 0057_6gsm_h.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999390 0.00244455 0.00249314 -1.49360317  
-0.00245288 0.99999140 0.00334522 -0.36462362  
-0.00248494 -0.00335131 0.99999130 1.17721721  
Axis -0.69213279 0.51451966 -0.50618349  
Axis point 0.00000000 388.68717064 148.49285133  
Rotation angle (degrees) 0.27717525  
Shift along axis 0.25027779  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h_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 216,241,180,287,360,275

> 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 14447 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 45675  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
45676  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
45677  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
45678  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
45679  
127 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
45928  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
45929  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
45930  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
45931  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
45932  
179 messages similar to the above omitted  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:24  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:25  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:40  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:41  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:64  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:110  
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:110  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:111  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:146  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:162  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:162  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:221  
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:272  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:364  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:365  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:373  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:417  
Atom C6 has no neighbors to form bonds with according to residue template for
C /2:423  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:433  
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:433  
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:459  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:468  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:468  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:627  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:627  
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:627  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:631  
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:631  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:795  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:795  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:830  
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:830  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:848  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1103  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1118  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /E:11  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /E:12  
Atom O has no neighbors to form bonds with according to residue template for
VAL /E:61  
Atom N has no neighbors to form bonds with according to residue template for
THR /E:141  
Atom O has no neighbors to form bonds with according to residue template for
THR /E:141  
Atom O has no neighbors to form bonds with according to residue template for
GLY /G:55  
Atom O has no neighbors to form bonds with according to residue template for
ILE /G:112  
Atom N has no neighbors to form bonds with according to residue template for
ILE /G:141  
Atom C has no neighbors to form bonds with according to residue template for
ILE /G:141  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /G:152  
Atom N has no neighbors to form bonds with according to residue template for
GLU /N:86  
Atom O has no neighbors to form bonds with according to residue template for
GLU /N:86  
Atom N has no neighbors to form bonds with according to residue template for
VAL /N:132  
Atom N has no neighbors to form bonds with according to residue template for
ASN /X:22  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /X:22  
Atom N has no neighbors to form bonds with according to residue template for
TRP /X:24  
Atom N has no neighbors to form bonds with according to residue template for
LYS /X:50  
Atom N has no neighbors to form bonds with according to residue template for
UNK /o:703  
Atom N has no neighbors to form bonds with according to residue template for
LEU /p:189  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /p:243  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /p:243  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /p:445  
  
Chain information for 0057_6gsm_I.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
E | 40S ribosomal protein S4  
G | 40S ribosomal protein S6  
I | 40S ribosomal protein S8  
J | KLLA0E23673p  
L | KLLA0A10483p  
N | KLLA0F18040p  
X | KLLA0B11231p  
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_I.mrc

Opened 0057_6gsm_I.mrc as #2, grid size 72,120,96, pixel 1, shown at level
0.144, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_I.cif (#1) to map 0057_6gsm_I.mrc (#2) using 14447
atoms  
average map value = 0.08325, steps = 64  
shifted from previous position = 0.639  
rotated from previous position = 0.171 degrees  
atoms outside contour = 13697, contour level = 0.14363  
  
Position of 0057_6gsm_I.cif (#1) relative to 0057_6gsm_I.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999700 0.00094952 -0.00225603 -0.15605800  
-0.00094564 0.99999807 0.00172043 -0.49124166  
0.00225766 -0.00171829 0.99999598 -0.43873210  
Axis -0.57480111 -0.75448682 -0.31678593  
Axis point 110.38476831 0.00000000 83.37759510  
Rotation angle (degrees) 0.17138502  
Shift along axis 0.59932182  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I_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 192,95,185,327,198,264

> 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 14398 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 45481  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
45482  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
45483  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
45484  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
45485  
121 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
45734  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
45735  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
45736  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
45737  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
45738  
141 messages similar to the above omitted  
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:920  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:923  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:987  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1145  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1145  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1280  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1286  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1286  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1287  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1287  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1306  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1308  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1308  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1460  
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1462  
Atom C6 has no neighbors to form bonds with according to residue template for
C /2:1463  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1526  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1756  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1756  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1783  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1783  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1796  
Atom N has no neighbors to form bonds with according to residue template for
ARG /B:26  
Atom O has no neighbors to form bonds with according to residue template for
PHE /B:81  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /B:116  
Atom N has no neighbors to form bonds with according to residue template for
PHE /B:142  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /F:55  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /F:94  
Atom N has no neighbors to form bonds with according to residue template for
ASN /F:130  
Atom N has no neighbors to form bonds with according to residue template for
LEU /F:132  
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /F:133  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /O:124  
Atom O has no neighbors to form bonds with according to residue template for
VAL /S:28  
Atom N has no neighbors to form bonds with according to residue template for
ALA /S:31  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /S:31  
Atom CG has no neighbors to form bonds with according to residue template for
LEU /S:61  
Atom N has no neighbors to form bonds with according to residue template for
THR /S:62  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /S:62  
Atom N has no neighbors to form bonds with according to residue template for
VAL /Z:92  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /Z:92  
Atom N has no neighbors to form bonds with according to residue template for
SER /a:88  
Atom CB has no neighbors to form bonds with according to residue template for
SER /a:88  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /c:31  
Atom N has no neighbors to form bonds with according to residue template for
ASP /k:193  
Atom N has no neighbors to form bonds with according to residue template for
MET /k:211  
Atom SD has no neighbors to form bonds with according to residue template for
MET /k:211  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /k:234  
Atom O has no neighbors to form bonds with according to residue template for
PHE /k:435  
Atom CD2 has no neighbors to form bonds with according to residue template for
PHE /k:435  
Atom NE has no neighbors to form bonds with according to residue template for
ARG /k:474  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /k:474  
Atom C has no neighbors to form bonds with according to residue template for
ARG /l:167  
Atom CD has no neighbors to form bonds with according to residue template for
ARG /l:167  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /l:167  
Atom N has no neighbors to form bonds with according to residue template for
ILE /p:116  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /p:118  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /p:118  
Atom C has no neighbors to form bonds with according to residue template for
LEU /p:127  
  
Chain information for 0057_6gsm_j.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
F | KLLA0D10659p  
O | 40S ribosomal protein S14  
Q | 40S ribosomal protein S16  
S | KLLA0B01562p  
T | KLLA0A07194p  
U | KLLA0F25542p  
Z | KLLA0B06182p  
a | 40S ribosomal protein S26  
c | 40S ribosomal protein S28  
i | Eukaryotic translation initiation factor 1A  
j | Eukaryotic translation initiation factor 2 subunit alpha  
k | Eukaryotic translation initiation factor 2 subunit gamma  
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  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j.mrc

Opened 0057_6gsm_j.mrc as #2, grid size 136,104,80, pixel 1, shown at level
0.119, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_j.cif (#1) to map 0057_6gsm_j.mrc (#2) using 14398
atoms  
average map value = 0.06882, steps = 56  
shifted from previous position = 0.502  
rotated from previous position = 0.155 degrees  
atoms outside contour = 13409, contour level = 0.11916  
  
Position of 0057_6gsm_j.cif (#1) relative to 0057_6gsm_j.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999853 0.00013427 0.00170961 -0.74251221  
-0.00013069 0.99999780 -0.00209394 0.48762654  
-0.00170989 0.00209372 0.99999635 -0.29123892  
Axis 0.77364167 0.63172986 -0.04894843  
Axis point 0.00000000 145.53493310 308.78942974  
Rotation angle (degrees) 0.15506880  
Shift along axis -0.25213445  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j_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 211,155,169,314,226,240

> 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 12721 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 43790  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
43791  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
43792  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
43793  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
43794  
100 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
44043  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
44044  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
44045  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
44046  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
44047  
153 messages similar to the above omitted  
Atom O6 has no neighbors to form bonds with according to residue template for
1MG /1:9  
Atom OP2 has no neighbors to form bonds with according to residue template for
2MG /1:10  
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:22  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:10  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:10  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:15  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:15  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:571  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:571  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:617  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:620  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:621  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:621  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:623  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:623  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:899  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:909  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:910  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:939  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1108  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1133  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1133  
Atom C8 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
A /2:1141  
Atom OP2 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
C /2:1176  
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:1188  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1454  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1454  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1456  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1463  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1463  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1617  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1617  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1619  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1632  
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1744  
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1793  
Atom N has no neighbors to form bonds with according to residue template for
ARG /B:8  
Atom O has no neighbors to form bonds with according to residue template for
ARG /B:8  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /F:222  
Atom O has no neighbors to form bonds with according to residue template for
ARG /O:90  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /O:103  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /O:103  
Atom N has no neighbors to form bonds with according to residue template for
THR /S:140  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /S:140  
Atom O has no neighbors to form bonds with according to residue template for
CYS /X:71  
Atom N has no neighbors to form bonds with according to residue template for
VAL /X:120  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /X:120  
Atom O has no neighbors to form bonds with according to residue template for
ASN /a:8  
Atom N has no neighbors to form bonds with according to residue template for
VAL /a:18  
Atom O has no neighbors to form bonds with according to residue template for
VAL /a:18  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /a:21  
Atom O has no neighbors to form bonds with according to residue template for
LEU /a:71  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /a:71  
Atom N has no neighbors to form bonds with according to residue template for
ILE /a:83  
Atom N has no neighbors to form bonds with according to residue template for
ARG /h:21  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /h:21  
Atom CG has no neighbors to form bonds with according to residue template for
ARG /i:24  
Atom O has no neighbors to form bonds with according to residue template for
GLU /i:34  
Atom N has no neighbors to form bonds with according to residue template for
ASP /i:53  
Atom C has no neighbors to form bonds with according to residue template for
ASP /i:53  
Atom N has no neighbors to form bonds with according to residue template for
ASP /i:83  
Atom C has no neighbors to form bonds with according to residue template for
ASP /i:83  
Atom N has no neighbors to form bonds with according to residue template for
ARG /i:101  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /i:109  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /i:109  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /j:19  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /j:19  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /j:46  
Atom OE1 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
ARG /j:75  
Atom N has no neighbors to form bonds with according to residue template for
GLY /k:277  
Atom O has no neighbors to form bonds with according to residue template for
GLY /k:277  
Atom O has no neighbors to form bonds with according to residue template for
ILE /k:291  
Atom O has no neighbors to form bonds with according to residue template for
ASN /k:295  
Atom N has no neighbors to form bonds with according to residue template for
LYS /k:300  
Atom N has no neighbors to form bonds with according to residue template for
ILE /k:495  
Atom CD1 has no neighbors to form bonds with according to residue template for
TYR /p:248  
Atom OG has no neighbors to form bonds with according to residue template for
SER /p:275  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /p:284  
Atom CD1 has no neighbors to form bonds with according to residue template for
TRP /p:336  
Atom N has no neighbors to form bonds with according to residue template for
ASP /p:360  
Atom O has no neighbors to form bonds with according to residue template for
ASP /p:360  
Atom N has no neighbors to form bonds with according to residue template for
ALA /p:370  
Atom O has no neighbors to form bonds with according to residue template for
ALA /p:370  
Atom N has no neighbors to form bonds with according to residue template for
VAL /q:112  
  
Chain information for 0057_6gsm_m.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
B | 40S ribosomal protein S1  
F | KLLA0D10659p  
O | 40S ribosomal protein S14  
P | KLLA0F07843p  
Q | 40S ribosomal protein S16  
S | KLLA0B01562p  
X | KLLA0B11231p  
a | 40S ribosomal protein S26  
c | 40S ribosomal protein S28  
e | 40S ribosomal protein S30  
h | 60S ribosomal protein L41-A  
i | Eukaryotic translation initiation factor 1A  
j | Eukaryotic translation initiation factor 2 subunit alpha  
k | Eukaryotic translation initiation factor 2 subunit gamma  
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_m.mrc

Opened 0057_6gsm_m.mrc as #2, grid size 104,72,72, pixel 1, shown at level
0.134, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_m.cif (#1) to map 0057_6gsm_m.mrc (#2) using 12721
atoms  
average map value = 0.0659, steps = 112  
shifted from previous position = 0.523  
rotated from previous position = 0.124 degrees  
atoms outside contour = 12229, contour level = 0.13429  
  
Position of 0057_6gsm_m.cif (#1) relative to 0057_6gsm_m.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999779 0.00130994 0.00164375 -1.03339978  
-0.00130910 0.99999901 -0.00050917 0.23869542  
-0.00164441 0.00050701 0.99999852 0.15046608  
Axis 0.23496469 0.76030197 -0.60558444  
Axis point 34.81184266 0.00000000 606.93991431  
Rotation angle (degrees) 0.12389672  
Shift along axis -0.15245178  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m_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 144,82,144,231,169,223

> 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 13497 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 44599  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
44600  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
44601  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
44602  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
44603  
174 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
44852  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
44853  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
44854  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
44855  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
44856  
183 messages similar to the above omitted  
Atom O4' has no neighbors to form bonds with according to residue template for
G /1:43  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1158  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1158  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1159  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1197  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1448  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1617  
Atom N3 has no neighbors to form bonds with according to residue template for
C /2:1617  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /D:41  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /D:41  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /F:42  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /F:64  
Atom C has no neighbors to form bonds with according to residue template for
VAL /F:134  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /F:138  
Atom O has no neighbors to form bonds with according to residue template for
SER /F:142  
Atom N has no neighbors to form bonds with according to residue template for
ARG /F:159  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /F:222  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /F:222  
Atom C has no neighbors to form bonds with according to residue template for
ASN /K:28  
Atom CB has no neighbors to form bonds with according to residue template for
ASN /K:28  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /P:23  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /P:23  
Atom O has no neighbors to form bonds with according to residue template for
GLY /P:48  
Atom O has no neighbors to form bonds with according to residue template for
ILE /P:85  
Atom O has no neighbors to form bonds with according to residue template for
VAL /P:94  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /P:94  
Atom N has no neighbors to form bonds with according to residue template for
ARG /P:127  
Atom O has no neighbors to form bonds with according to residue template for
ARG /P:127  
Atom N has no neighbors to form bonds with according to residue template for
TRP /S:129  
Atom C has no neighbors to form bonds with according to residue template for
TRP /S:129  
Atom CB has no neighbors to form bonds with according to residue template for
TRP /S:129  
Atom CD1 has no neighbors to form bonds with according to residue template for
TRP /S:129  
Atom N has no neighbors to form bonds with according to residue template for
GLU /U:46  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /U:99  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /c:25  
Atom C has no neighbors to form bonds with according to residue template for
LYS /c:45  
Atom O has no neighbors to form bonds with according to residue template for
TYR /d:8  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /d:8  
Atom O has no neighbors to form bonds with according to residue template for
ILE /d:38  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /g:35  
Atom N has no neighbors to form bonds with according to residue template for
VAL /g:72  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /g:112  
Atom N has no neighbors to form bonds with according to residue template for
ALA /g:249  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /g:249  
Atom N has no neighbors to form bonds with according to residue template for
ARG /j:54  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /j:87  
  
Chain information for 0057_6gsm_T.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
D | KLLA0D08305p  
F | KLLA0D10659p  
K | KLLA0B08173p  
P | KLLA0F07843p  
Q | 40S ribosomal protein S16  
R | KLLA0B01474p  
S | KLLA0B01562p  
T | KLLA0A07194p  
U | KLLA0F25542p  
Z | KLLA0B06182p  
c | 40S ribosomal protein S28  
d | 40S ribosomal protein S29  
g | KLLA0E12277p  
j | Eukaryotic translation initiation factor 2 subunit alpha  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T.mrc

Opened 0057_6gsm_T.mrc as #2, grid size 88,88,80, pixel 1, shown at level
0.133, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_T.cif (#1) to map 0057_6gsm_T.mrc (#2) using 13497
atoms  
average map value = 0.07745, steps = 60  
shifted from previous position = 0.338  
rotated from previous position = 0.083 degrees  
atoms outside contour = 12958, contour level = 0.13258  
  
Position of 0057_6gsm_T.cif (#1) relative to 0057_6gsm_T.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999979 -0.00028336 0.00058636 -0.30702594  
0.00028412 0.99999912 -0.00129319 0.23254354  
-0.00058599 0.00129335 0.99999899 -0.30519742  
Axis 0.89315267 0.40482004 0.19595673  
Axis point -0.00000000 199.82647397 254.78106719  
Rotation angle (degrees) 0.08296346  
Shift along axis -0.23988825  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T_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 169,249,127,296,328,198

> 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 12319 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 43436  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
43437  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
43438  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
43439  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
43440  
161 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
43689  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
43690  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
43691  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
43692  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
43693  
187 messages similar to the above omitted  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:23  
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:28  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:29  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:77  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:173  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:271  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:290  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:290  
Atom C4' has no neighbors to form bonds with according to residue template for
C /2:297  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:297  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:359  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:389  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:392  
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:395  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:396  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:398  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:508  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:542  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:592  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:593  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1659  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1684  
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1711  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1720  
Atom N has no neighbors to form bonds with according to residue template for
GLN /C:155  
Atom O has no neighbors to form bonds with according to residue template for
GLN /C:155  
Atom CB has no neighbors to form bonds with according to residue template for
PRO /C:178  
Atom O has no neighbors to form bonds with according to residue template for
ALA /E:2  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /E:2  
Atom N has no neighbors to form bonds with according to residue template for
TYR /E:121  
Atom O has no neighbors to form bonds with according to residue template for
TYR /E:121  
Atom N has no neighbors to form bonds with according to residue template for
PHE /G:145  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /G:153  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /G:153  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /G:159  
Atom O has no neighbors to form bonds with according to residue template for
GLU /J:183  
Atom O has no neighbors to form bonds with according to residue template for
ARG /p:663  
Atom N has no neighbors to form bonds with according to residue template for
ALA /p:692  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /p:692  
  
Chain information for 0057_6gsm_Y.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
C | KLLA0F09812p  
E | 40S ribosomal protein S4  
G | 40S ribosomal protein S6  
J | KLLA0E23673p  
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  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y.mrc

Opened 0057_6gsm_Y.mrc as #2, grid size 128,80,72, pixel 1, shown at level
0.142, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_Y.cif (#1) to map 0057_6gsm_Y.mrc (#2) using 12319
atoms  
average map value = 0.08353, steps = 48  
shifted from previous position = 0.466  
rotated from previous position = 0.137 degrees  
atoms outside contour = 11679, contour level = 0.14216  
  
Position of 0057_6gsm_Y.cif (#1) relative to 0057_6gsm_Y.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999809 -0.00071326 -0.00182141 0.23329565  
0.00071574 0.99999882 0.00136215 -0.76507248  
0.00182043 -0.00136345 0.99999741 0.02693523  
Axis -0.57164385 -0.76380649 0.29970477  
Axis point 61.17022831 0.00000000 272.10136371  
Rotation angle (degrees) 0.13659378  
Shift along axis 0.45907793  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y_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 144,95,177,239,198,256

> 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 16573 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F.cif  
---  
warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
near line 47739  
Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
47740  
Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
47741  
Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
47742  
Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
47743  
112 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
line 47997  
Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
line 47998  
Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
line 47999  
Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
line 48000  
Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
line 48001  
139 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /1:22  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /1:22  
Atom C5' has no neighbors to form bonds with according to residue template for
G /1:22  
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:22  
Atom O3' has no neighbors to form bonds with according to residue template for
C /1:23  
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:24  
Atom O4 has no neighbors to form bonds with according to residue template for
U /1:45  
Atom C5 has no neighbors to form bonds with according to residue template for
U /1:45  
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:899  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:987  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:987  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:999  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1145  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1145  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1273  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1278  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1347  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1354  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1355  
Atom C2' has no neighbors to form bonds with according to residue template for
A /2:1371  
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:1520  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1598  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1598  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1783  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1783  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1796  
Atom N has no neighbors to form bonds with according to residue template for
TYR /A:81  
Atom CB has no neighbors to form bonds with according to residue template for
GLN /A:83  
Atom N has no neighbors to form bonds with according to residue template for
VAL /B:3  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /B:107  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /B:116  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /D:126  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /D:126  
Atom N has no neighbors to form bonds with according to residue template for
ILE /D:138  
Atom N has no neighbors to form bonds with according to residue template for
MET /D:150  
Atom N has no neighbors to form bonds with according to residue template for
ASP /D:154  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /D:186  
Atom N has no neighbors to form bonds with according to residue template for
GLU /D:214  
Atom N has no neighbors to form bonds with according to residue template for
LYS /O:72  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /O:124  
Atom N has no neighbors to form bonds with according to residue template for
LEU /S:18  
Atom O has no neighbors to form bonds with according to residue template for
LEU /S:18  
Atom O has no neighbors to form bonds with according to residue template for
LYS /T:38  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /T:38  
Atom N has no neighbors to form bonds with according to residue template for
ASN /U:36  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /U:36  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /U:36  
Atom N has no neighbors to form bonds with according to residue template for
LYS /U:61  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /U:67  
Atom N has no neighbors to form bonds with according to residue template for
SER /a:57  
Atom OG has no neighbors to form bonds with according to residue template for
SER /a:57  
Atom N has no neighbors to form bonds with according to residue template for
SER /a:88  
Atom CB has no neighbors to form bonds with according to residue template for
SER /a:88  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /d:48  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /d:48  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /g:35  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /g:48  
Atom N has no neighbors to form bonds with according to residue template for
VAL /g:72  
Atom N has no neighbors to form bonds with according to residue template for
ALA /g:249  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /g:249  
Atom N has no neighbors to form bonds with according to residue template for
LYS /g:268  
Atom N has no neighbors to form bonds with according to residue template for
LEU /g:299  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /g:299  
Atom CB has no neighbors to form bonds with according to residue template for
TYR /j:9  
Atom OG has no neighbors to form bonds with according to residue template for
SER /j:91  
Atom N has no neighbors to form bonds with according to residue template for
LEU /j:123  
Atom C has no neighbors to form bonds with according to residue template for
LEU /j:123  
Atom NE1 has no neighbors to form bonds with according to residue template for
TRP /j:132  
Atom O has no neighbors to form bonds with according to residue template for
ILE /l:173  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /m:36  
  
Chain information for 0057_6gsm_F.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  
O | 40S ribosomal protein S14  
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_F.mrc

Opened 0057_6gsm_F.mrc as #2, grid size 96,104,80, pixel 1, shown at level
0.132, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_F.cif (#1) to map 0057_6gsm_F.mrc (#2) using 16573
atoms  
average map value = 0.07465, steps = 48  
shifted from previous position = 0.482  
rotated from previous position = 0.311 degrees  
atoms outside contour = 15915, contour level = 0.13241  
  
Position of 0057_6gsm_F.cif (#1) relative to 0057_6gsm_F.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999869 -0.00155151 -0.00047107 0.19682187  
0.00154904 0.99998536 -0.00518424 0.71416720  
0.00047911 0.00518351 0.99998645 -1.35461568  
Axis 0.95440247 -0.08746900 0.28542090  
Axis point -0.00000000 247.29302550 132.65108473  
Rotation angle (degrees) 0.31120585  
Shift along axis -0.26125584  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F_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 187,227,189,274,338,292

> 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 20625 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 51957  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
51958  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
51959  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
51960  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
51961  
107 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
52210  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
52211  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
52212  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
52213  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
52214  
152 messages similar to the above omitted  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:20  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:24  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:24  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:26  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:43  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:47  
Atom C6 has no neighbors to form bonds with according to residue template for
C /2:90  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:135  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:135  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:196  
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:196  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:196  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:229  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:229  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:273  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:273  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:281  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:286  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:286  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:286  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:286  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:287  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:287  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:288  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:387  
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:571  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:571  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:619  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:695  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:695  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:695  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:729  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:729  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:731  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:786  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:949  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1019  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1019  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1048  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1048  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1109  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1109  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1125  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1647  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1678  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1706  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1706  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1720  
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:1744  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1744  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /C:163  
Atom O has no neighbors to form bonds with according to residue template for
PRO /C:178  
Atom N has no neighbors to form bonds with according to residue template for
LEU /C:192  
Atom CB has no neighbors to form bonds with according to residue template for
LEU /C:192  
Atom N has no neighbors to form bonds with according to residue template for
ARG /C:210  
Atom CG has no neighbors to form bonds with according to residue template for
ARG /C:210  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /E:81  
Atom N has no neighbors to form bonds with according to residue template for
GLU /E:250  
Atom C has no neighbors to form bonds with according to residue template for
GLU /E:250  
Atom CB has no neighbors to form bonds with according to residue template for
GLU /E:250  
Atom O has no neighbors to form bonds with according to residue template for
ARG /G:88  
Atom O has no neighbors to form bonds with according to residue template for
ARG /G:183  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /G:183  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /G:184  
Atom C has no neighbors to form bonds with according to residue template for
ARG /H:96  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /H:96  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /H:96  
Atom N has no neighbors to form bonds with according to residue template for
VAL /H:121  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /H:121  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /I:138  
Atom O has no neighbors to form bonds with according to residue template for
LYS /J:16  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /N:104  
Atom N has no neighbors to form bonds with according to residue template for
ASN /N:105  
Atom O has no neighbors to form bonds with according to residue template for
ASN /N:105  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /W:14  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /W:26  
Atom C has no neighbors to form bonds with according to residue template for
LYS /W:71  
Atom O has no neighbors to form bonds with according to residue template for
ASN /X:79  
Atom O has no neighbors to form bonds with according to residue template for
ALA /X:113  
Atom N has no neighbors to form bonds with according to residue template for
LYS /b:72  
Atom O has no neighbors to form bonds with according to residue template for
LYS /b:72  
Atom N has no neighbors to form bonds with according to residue template for
ARG /h:23  
Atom O has no neighbors to form bonds with according to residue template for
UNK /o:734  
Atom C has no neighbors to form bonds with according to residue template for
ASP /p:360  
Atom CA has no neighbors to form bonds with according to residue template for
ASP /p:397  
Atom N has no neighbors to form bonds with according to residue template for
ARG /p:677  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /p:677  
Atom N has no neighbors to form bonds with according to residue template for
LYS /q:113  
  
Chain information for 0057_6gsm_L.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  
W | 40S ribosomal protein S22  
X | KLLA0B11231p  
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_L.mrc

Opened 0057_6gsm_L.mrc as #2, grid size 88,112,104, pixel 1, shown at level
0.147, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_L.cif (#1) to map 0057_6gsm_L.mrc (#2) using 20625
atoms  
average map value = 0.0855, steps = 64  
shifted from previous position = 0.562  
rotated from previous position = 0.106 degrees  
atoms outside contour = 19726, contour level = 0.14692  
  
Position of 0057_6gsm_L.cif (#1) relative to 0057_6gsm_L.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999903 0.00135370 -0.00033389 -0.56069105  
-0.00135329 0.99999833 0.00122632 -0.32874382  
0.00033555 -0.00122587 0.99999919 -0.08200758  
Axis -0.66036488 -0.18027934 -0.72898394  
Axis point -177.95394095 175.36755179 0.00000000  
Rotation angle (degrees) 0.10638074  
Shift along axis 0.48930860  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L_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 203,162,172,250,217,227

> 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 4594 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 35563  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
35564  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
35565  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
35566  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
35567  
172 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
35816  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
35817  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
35818  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
35819  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
35820  
187 messages similar to the above omitted  
Atom O5' has no neighbors to form bonds with according to residue template for
C /1:11  
Atom N6 has no neighbors to form bonds with according to residue template for
A /1:28  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:11  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:12  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:579  
Atom C2' has no neighbors to form bonds with according to residue template for
U /2:580  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:906  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:991  
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:993  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1029  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1087  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1137  
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1137  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1137  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1152  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1156  
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:1156  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1159  
Atom C2' has no neighbors to form bonds with according to residue template for
G /2:1187  
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:1196  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1272  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1274  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1424  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1462  
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:1577  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1578  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1749  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1749  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1751  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1751  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1773  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1784  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1784  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1788  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1794  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1794  
Atom N has no neighbors to form bonds with according to residue template for
ILE /X:68  
Atom C has no neighbors to form bonds with according to residue template for
THR /c:19  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /c:19  
Atom N has no neighbors to form bonds with according to residue template for
GLY /c:23  
Atom O has no neighbors to form bonds with according to residue template for
GLY /c:23  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /c:25  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /c:25  
Atom N has no neighbors to form bonds with according to residue template for
LEU /h:13  
Atom O has no neighbors to form bonds with according to residue template for
ASN /i:55  
Atom N has no neighbors to form bonds with according to residue template for
LEU /i:78  
Atom N has no neighbors to form bonds with according to residue template for
VAL /j:90  
Atom N has no neighbors to form bonds with according to residue template for
ILE /l:180  
Atom N has no neighbors to form bonds with according to residue template for
THR /m:41  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /m:41  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /m:41  
Atom N has no neighbors to form bonds with according to residue template for
ASP /m:61  
Atom C has no neighbors to form bonds with according to residue template for
ASP /m:61  
  
Chain information for 0057_6gsm_3.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
C | KLLA0F09812p  
D | KLLA0D08305p  
F | KLLA0D10659p  
O | 40S ribosomal protein S14  
Q | 40S ribosomal protein S16  
U | KLLA0F25542p  
X | KLLA0B11231p  
a | 40S ribosomal protein S26  
c | 40S ribosomal protein S28  
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  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3.mrc

Opened 0057_6gsm_3.mrc as #2, grid size 48,56,56, pixel 1, shown at level
0.147, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_3.cif (#1) to map 0057_6gsm_3.mrc (#2) using 4594 atoms  
average map value = 0.0782, steps = 56  
shifted from previous position = 0.482  
rotated from previous position = 0.264 degrees  
atoms outside contour = 4481, contour level = 0.14686  
  
Position of 0057_6gsm_3.cif (#1) relative to 0057_6gsm_3.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999048 0.00086917 -0.00427518 0.27803584  
-0.00087555 0.99999851 -0.00149093 0.24639436  
0.00427388 0.00149466 0.99998975 -1.25590328  
Axis 0.32374789 -0.92703488 -0.18919205  
Axis point 289.60036558 0.00000000 56.87772451  
Rotation angle (degrees) 0.26419021  
Shift along axis 0.09920427  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3_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 151,212,105,246,299,232

> 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 20634 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J.cif  
---  
warnings | Invalid residue range for struct_conf "HELX7": invalid chain "E",
near line 51987  
Invalid residue range for struct_conf "HELX8": invalid chain "E", near line
51988  
Invalid residue range for struct_conf "HELX9": invalid chain "E", near line
51989  
Invalid residue range for struct_conf "HELX10": invalid chain "E", near line
51990  
Invalid residue range for struct_conf "HELX11": invalid chain "E", near line
51991  
147 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 8": invalid chain "E", near line
52241  
Invalid sheet range for struct_sheet_range "? 9": invalid chain "E", near line
52242  
Invalid sheet range for struct_sheet_range "? 10": invalid chain "E", near
line 52243  
Invalid sheet range for struct_sheet_range "? 11": invalid chain "E", near
line 52244  
Invalid sheet range for struct_sheet_range "? 12": invalid chain "E", near
line 52245  
130 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:11  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:49  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:295  
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:295  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:322  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:325  
Atom C4' has no neighbors to form bonds with according to residue template for
A /2:327  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:328  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:328  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:430  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:431  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:432  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:565  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:629  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:666  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:707  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:722  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:722  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:745  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:805  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:978  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:978  
Atom C4' has no neighbors to form bonds with according to residue template for
G /2:979  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:979  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:979  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1021  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1021  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1032  
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:1038  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1038  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1088  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1142  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1294  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1294  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1299  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1738  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1747  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1747  
Atom C2 has no neighbors to form bonds with according to residue template for
A /2:1747  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1753  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1753  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1770  
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
A /2:1788  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1788  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1790  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /A:59  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /A:108  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /A:108  
Atom O has no neighbors to form bonds with according to residue template for
LEU /A:177  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /C:48  
Atom N has no neighbors to form bonds with according to residue template for
VAL /C:91  
Atom CD1 has no neighbors to form bonds with according to residue template for
PHE /C:103  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /C:122  
Atom N has no neighbors to form bonds with according to residue template for
GLY /C:128  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /C:250  
Atom N has no neighbors to form bonds with according to residue template for
PRO /E:35  
Atom C has no neighbors to form bonds with according to residue template for
ASP /E:79  
Atom O has no neighbors to form bonds with according to residue template for
HIS /E:142  
Atom C has no neighbors to form bonds with according to residue template for
LEU /E:238  
Atom CA has no neighbors to form bonds with according to residue template for
GLY /H:145  
Atom O has no neighbors to form bonds with according to residue template for
GLY /H:145  
Atom N has no neighbors to form bonds with according to residue template for
THR /L:72  
Atom O has no neighbors to form bonds with according to residue template for
THR /L:72  
Atom C has no neighbors to form bonds with according to residue template for
ARG /L:87  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /V:64  
Atom O has no neighbors to form bonds with according to residue template for
LEU /V:69  
Atom O has no neighbors to form bonds with according to residue template for
LYS /Y:52  
Atom N has no neighbors to form bonds with according to residue template for
VAL /Y:75  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /Y:75  
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /Y:76  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /Y:76  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /Y:96  
Atom N has no neighbors to form bonds with according to residue template for
TRP /h:5  
Atom CD has no neighbors to form bonds with according to residue template for
ARG /i:57  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /i:57  
  
Chain information for 0057_6gsm_J.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
A | 40S ribosomal protein S0  
C | KLLA0F09812p  
E | 40S ribosomal protein S4  
H | 40S ribosomal protein S7  
I | 40S ribosomal protein S8  
J | KLLA0E23673p  
L | KLLA0A10483p  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S22  
X | KLLA0B11231p  
Y | 40S ribosomal protein S24  
a | 40S ribosomal protein S26  
e | 40S ribosomal protein S30  
h | 60S ribosomal protein L41-A  
i | Eukaryotic translation initiation factor 1A  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J.mrc

Opened 0057_6gsm_J.mrc as #2, grid size 96,88,128, pixel 1, shown at level
0.146, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_J.cif (#1) to map 0057_6gsm_J.mrc (#2) using 20634
atoms  
average map value = 0.08539, steps = 48  
shifted from previous position = 0.283  
rotated from previous position = 0.0807 degrees  
atoms outside contour = 19712, contour level = 0.14584  
  
Position of 0057_6gsm_J.cif (#1) relative to 0057_6gsm_J.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999926 0.00084597 0.00087723 -0.52834288  
-0.00084659 0.99999939 0.00070453 -0.19287997  
-0.00087663 -0.00070527 0.99999937 0.28359637  
Axis -0.50068506 0.62287955 -0.60111192  
Axis point 305.17755694 0.00000000 617.43129214  
Rotation angle (degrees) 0.08066466  
Shift along axis -0.02608076  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J_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 151,200,212,230,263,315

> 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 13648 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 44712  
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
44713  
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
44714  
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
44715  
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
44716  
111 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 44969  
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 44970  
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 44971  
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 44972  
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 44973  
189 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:306  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:306  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:308  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:308  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:348  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:348  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:349  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:637  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:639  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:794  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:794  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1023  
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:1023  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1113  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1302  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1302  
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 O3' has no neighbors to form bonds with according to residue template for
U /2:1626  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1772  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1786  
Atom N has no neighbors to form bonds with according to residue template for
THR /A:10  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /A:88  
Atom ND1 has no neighbors to form bonds with according to residue template for
HIS /A:92  
Atom N has no neighbors to form bonds with according to residue template for
GLY /A:100  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /A:179  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /B:122  
Atom CE has no neighbors to form bonds with according to residue template for
LYS /B:145  
Atom N has no neighbors to form bonds with according to residue template for
LEU /B:172  
Atom C has no neighbors to form bonds with according to residue template for
LEU /B:172  
Atom CB has no neighbors to form bonds with according to residue template for
LEU /B:172  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /B:172  
Atom CE has no neighbors to form bonds with according to residue template for
MET /C:245  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /H:87  
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /H:87  
Atom O has no neighbors to form bonds with according to residue template for
ARG /H:114  
Atom O has no neighbors to form bonds with according to residue template for
HIS /L:104  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /N:99  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /N:99  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /N:100  
Atom CE has no neighbors to form bonds with according to residue template for
LYS /N:100  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /N:140  
Atom N has no neighbors to form bonds with according to residue template for
ARG /O:133  
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 C has no neighbors to form bonds with according to residue template for
VAL /V:13  
Atom N has no neighbors to form bonds with according to residue template for
VAL /V:39  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /q:393  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /q:448  
Atom NE1 has no neighbors to form bonds with according to residue template for
TRP /q:456  
Atom CZ2 has no neighbors to form bonds with according to residue template for
TRP /q:456  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /q:484  
Atom CA has no neighbors to form bonds with according to residue template for
GLN /q:517  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /q:654  
  
Chain information for 0057_6gsm_b.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
A | 40S ribosomal protein S0  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
H | 40S ribosomal protein S7  
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  
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 80,64,104, pixel 1, shown at level
0.145, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_b.cif (#1) to map 0057_6gsm_b.mrc (#2) using 13648
atoms  
average map value = 0.06975, steps = 120  
shifted from previous position = 0.477  
rotated from previous position = 0.155 degrees  
atoms outside contour = 13183, contour level = 0.1446  
  
Position of 0057_6gsm_b.cif (#1) relative to 0057_6gsm_b.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999867 0.00068419 -0.00147724 0.10063725  
-0.00068737 0.99999744 -0.00215405 0.39911254  
0.00147576 0.00215506 0.99999659 -1.14122012  
Axis 0.79784835 -0.54676044 -0.25395084  
Axis point 0.00000000 512.00866074 223.23098321  
Rotation angle (degrees) 0.15472488  
Shift along axis 0.15188813  
  

> 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 163,124,197,234,203,268

> 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 9480 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c.cif  
---  
warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
near line 40502  
Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
40503  
Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
40504  
Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
40505  
Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
40506  
134 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
line 40760  
Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
line 40761  
Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
line 40762  
Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
line 40763  
Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
line 40764  
163 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
C /2:882  
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:887  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:900  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:900  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:905  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:927  
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 O3' has no neighbors to form bonds with according to residue template for
A /2:1320  
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 O4' has no neighbors to form bonds with according to residue template for
C /2:1338  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1532  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1532  
Atom C1' has no neighbors to form bonds with according to residue template for
G /2:1532  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1578  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1607  
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 C4' has no neighbors to form bonds with according to residue template for
A /2:1631  
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1769  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1782  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1791  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1791  
Atom O has no neighbors to form bonds with according to residue template for
ILE /A:111  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /A:111  
Atom CD2 has no neighbors to form bonds with according to residue template for
HIS /A:168  
Atom O has no neighbors to form bonds with according to residue template for
TYR /A:204  
Atom O4 has no neighbors to form bonds with according to residue template for
U /3:30  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /B:46  
Atom N has no neighbors to form bonds with according to residue template for
VAL /B:84  
Atom O has no neighbors to form bonds with according to residue template for
VAL /B:84  
Atom SD has no neighbors to form bonds with according to residue template for
MET /B:103  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLN /B:149  
Atom CA has no neighbors to form bonds with according to residue template for
VAL /B:150  
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 /F:25  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /F:25  
Atom O has no neighbors to form bonds with according to residue template for
GLU /F:34  
Atom CD has no neighbors to form bonds with according to residue template for
ARG /F:104  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /F:104  
Atom N has no neighbors to form bonds with according to residue template for
ASP /F:128  
Atom C has no neighbors to form bonds with according to residue template for
ASP /F:128  
Atom N has no neighbors to form bonds with according to residue template for
MET /O:46  
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 C has no neighbors to form bonds with according to residue template for
ALA /Q:20  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /Q:20  
Atom N has no neighbors to form bonds with according to residue template for
GLN /Q:40  
Atom N has no neighbors to form bonds with according to residue template for
GLN /Q:77  
Atom N has no neighbors to form bonds with according to residue template for
LEU /Q:89  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /Q:105  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /R:18  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /R:18  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /R:54  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /R:55  
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /R:61  
Atom O has no neighbors to form bonds with according to residue template for
LYS /a:32  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /a:32  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /a:34  
Atom N has no neighbors to form bonds with according to residue template for
ASP /j:18  
Atom O has no neighbors to form bonds with according to residue template for
ASP /j:18  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /j:23  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /j:63  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /j:64  
Atom N has no neighbors to form bonds with according to residue template for
VAL /o:48  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /o:76  
  
Chain information for 0057_6gsm_c.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  
O | 40S ribosomal protein S14  
Q | 40S ribosomal protein S16  
R | KLLA0B01474p  
Z | KLLA0B06182p  
a | 40S ribosomal protein S26  
c | 40S ribosomal protein S28  
g | KLLA0E12277p  
j | Eukaryotic translation initiation factor 2 subunit alpha  
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c.mrc

Opened 0057_6gsm_c.mrc as #2, grid size 72,80,72, pixel 1, shown at level
0.137, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_c.cif (#1) to map 0057_6gsm_c.mrc (#2) using 9480 atoms  
average map value = 0.07507, steps = 48  
shifted from previous position = 0.58  
rotated from previous position = 0.323 degrees  
atoms outside contour = 9159, contour level = 0.13696  
  
Position of 0057_6gsm_c.cif (#1) relative to 0057_6gsm_c.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999841 -0.00143913 0.00105503 -0.05309246  
0.00144474 0.99998470 -0.00534025 0.88891144  
-0.00104733 0.00534177 0.99998518 -1.26219123  
Axis 0.94846552 0.18667082 0.25606087  
Axis point 0.00000000 226.81472737 173.06242894  
Rotation angle (degrees) 0.32264642  
Shift along axis -0.20762033  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c_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 199,164,139,278,243,210

> 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 10393 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 41478  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
41479  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
41480  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
41481  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
41482  
130 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
41731  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
41732  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
41733  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
41734  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
41735  
155 messages similar to the above omitted  
Atom O2 has no neighbors to form bonds with according to residue template for
C /1:11  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /1:12  
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:12  
Atom N2 has no neighbors to form bonds with according to residue template for
G /1:24  
Atom N3 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 /1:29  
Atom O2 has no neighbors to form bonds with according to residue template for
C /1:69  
Atom O4' has no neighbors to form bonds with according to residue template for
U /1:72  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:4  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:13  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:540  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:544  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:544  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:555  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:556  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:557  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:588  
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:588  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:601  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:609  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:609  
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:612  
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1085  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1085  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1114  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1142  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1149  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1149  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1158  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1175  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1175  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1176  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1184  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1199  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1213  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1214  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1215  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1216  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1264  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1280  
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:1281  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1281  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1282  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1423  
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:1435  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1436  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1462  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1575  
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1575  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1575  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1622  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1623  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1627  
Atom N1 has no neighbors to form bonds with according to residue template for
G /2:1627  
Atom N2 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
U /2:1740  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1740  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1740  
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1780  
Atom N has no neighbors to form bonds with according to residue template for
ALA /C:97  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /J:23  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /J:23  
Atom N has no neighbors to form bonds with according to residue template for
LYS /U:77  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /X:39  
Atom N has no neighbors to form bonds with according to residue template for
LYS /X:78  
Atom C has no neighbors to form bonds with according to residue template for
LYS /X:78  
Atom N has no neighbors to form bonds with according to residue template for
LYS /f:90  
Atom O has no neighbors to form bonds with according to residue template for
LYS /f:90  
Atom O has no neighbors to form bonds with according to residue template for
ILE /l:141  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /l:141  
Atom CD has no neighbors to form bonds with according to residue template for
ARG /l:253  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /m:54  
Atom CA has no neighbors to form bonds with according to residue template for
LEU /m:55  
Atom O has no neighbors to form bonds with according to residue template for
LEU /m:55  
Atom N has no neighbors to form bonds with according to residue template for
ASN /m:67  
Atom O has no neighbors to form bonds with according to residue template for
ASN /m:67  
Atom N has no neighbors to form bonds with according to residue template for
TRP /p:315  
Atom N has no neighbors to form bonds with according to residue template for
GLY /p:320  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /p:480  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /p:480  
  
Chain information for 0057_6gsm_i.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
C | KLLA0F09812p  
D | KLLA0D08305p  
J | KLLA0E23673p  
Q | 40S ribosomal protein S16  
U | KLLA0F25542p  
X | KLLA0B11231p  
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  
k | Eukaryotic translation initiation factor 2 subunit gamma  
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  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i.mrc

Opened 0057_6gsm_i.mrc as #2, grid size 80,80,72, pixel 1, shown at level
0.139, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_i.cif (#1) to map 0057_6gsm_i.mrc (#2) using 10393
atoms  
average map value = 0.07196, steps = 56  
shifted from previous position = 0.474  
rotated from previous position = 0.143 degrees  
atoms outside contour = 9995, contour level = 0.13898  
  
Position of 0057_6gsm_i.cif (#1) relative to 0057_6gsm_i.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999692 0.00018283 0.00247368 -0.90601607  
-0.00018207 0.99999994 -0.00030762 -0.12008924  
-0.00247373 0.00030717 0.99999689 0.50653629  
Axis 0.12298613 0.98972007 -0.07299718  
Axis point 196.43577144 0.00000000 353.21954976  
Rotation angle (degrees) 0.14320519  
Shift along axis -0.26725786  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i_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 183,191,137,270,278,248

> 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 24244 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X.cif  
---  
warnings | Invalid residue range for struct_conf "HELX32": invalid chain "I",
near line 55763  
Invalid residue range for struct_conf "HELX33": invalid chain "I", near line
55764  
Invalid residue range for struct_conf "HELX34": invalid chain "I", near line
55765  
Invalid residue range for struct_conf "HELX35": invalid chain "I", near line
55766  
Invalid residue range for struct_conf "HELX36": invalid chain "I", near line
55767  
58 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 47": invalid chain "I", near
line 56031  
Invalid sheet range for struct_sheet_range "? 48": invalid chain "I", near
line 56032  
Invalid sheet range for struct_sheet_range "? 79": invalid chain "P", near
line 56063  
Invalid sheet range for struct_sheet_range "? 80": invalid chain "P", near
line 56064  
Invalid sheet range for struct_sheet_range "? 86": invalid chain "S", near
line 56070  
104 messages similar to the above omitted  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:325  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:325  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:338  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:341  
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:341  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:391  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:415  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:459  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:479  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:481  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:525  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:809  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:888  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:925  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:926  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:928  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:930  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:930  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:936  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:937  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:943  
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:943  
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:964  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1001  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1001  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1002  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1002  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1016  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1043  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1071  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1150  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1290  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1318  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1421  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1435  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1435  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1623  
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:1623  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1623  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1635  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1667  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /3:29  
Atom O has no neighbors to form bonds with according to residue template for
LEU /C:159  
Atom N has no neighbors to form bonds with according to residue template for
LEU /C:195  
Atom O has no neighbors to form bonds with according to residue template for
VAL /C:198  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /C:198  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /C:198  
Atom CE has no neighbors to form bonds with according to residue template for
MET /D:105  
Atom N has no neighbors to form bonds with according to residue template for
TYR /D:120  
Atom N has no neighbors to form bonds with according to residue template for
ALA /D:153  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /D:153  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /D:173  
Atom N has no neighbors to form bonds with according to residue template for
SER /H:106  
Atom N has no neighbors to form bonds with according to residue template for
GLN /H:110  
Atom O has no neighbors to form bonds with according to residue template for
GLN /H:110  
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
LEU /J:93  
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
PHE /K:54  
Atom CE1 has no neighbors to form bonds with according to residue template for
PHE /K:54  
Atom NE has no neighbors to form bonds with according to residue template for
ARG /L:116  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /L:116  
Atom O has no neighbors to form bonds with according to residue template for
VAL /L:125  
Atom C has no neighbors to form bonds with according to residue template for
SER /L:132  
Atom N has no neighbors to form bonds with according to residue template for
ARG /L:136  
Atom CA has no neighbors to form bonds with according to residue template for
GLY /L:147  
Atom O has no neighbors to form bonds with according to residue template for
GLY /L:147  
Atom O has no neighbors to form bonds with according to residue template for
ILE /N:116  
Atom O has no neighbors to form bonds with according to residue template for
THR /O:89  
Atom N has no neighbors to form bonds with according to residue template for
SER /O:125  
Atom OG has no neighbors to form bonds with according to residue template for
SER /O:125  
Atom N has no neighbors to form bonds with according to residue template for
GLN /W:39  
Atom N has no neighbors to form bonds with according to residue template for
MET /W:41  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /W:69  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /W:69  
Atom O has no neighbors to form bonds with according to residue template for
ASN /Y:31  
Atom N has no neighbors to form bonds with according to residue template for
ASN /a:25  
Atom C has no neighbors to form bonds with according to residue template for
ASN /a:25  
Atom CB has no neighbors to form bonds with according to residue template for
ASN /a:25  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /a:25  
Atom N has no neighbors to form bonds with according to residue template for
MET /a:39  
Atom N has no neighbors to form bonds with according to residue template for
GLN /a:99  
Atom N has no neighbors to form bonds with according to residue template for
VAL /e:47  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /e:47  
Atom O has no neighbors to form bonds with according to residue template for
ARG /m:36  
Atom O has no neighbors to form bonds with according to residue template for
THR /m:38  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /m:38  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /m:47  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /m:67  
Atom O has no neighbors to form bonds with according to residue template for
ILE /m:103  
Atom O has no neighbors to form bonds with according to residue template for
PRO /p:88  
Atom N has no neighbors to form bonds with according to residue template for
ILE /p:116  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /p:116  
Atom N has no neighbors to form bonds with according to residue template for
ASP /p:380  
Atom N has no neighbors to form bonds with according to residue template for
GLN /p:444  
Atom O has no neighbors to form bonds with according to residue template for
GLN /p:444  
Atom N has no neighbors to form bonds with according to residue template for
GLU /p:455  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /p:468  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /p:592  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /p:592  
Atom N has no neighbors to form bonds with according to residue template for
VAL /p:595  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /p:595  
  
Chain information for 0057_6gsm_X.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
D | KLLA0D08305p  
E | 40S ribosomal protein S4  
H | 40S ribosomal protein S7  
I | 40S ribosomal protein S8  
J | KLLA0E23673p  
K | KLLA0B08173p  
L | KLLA0A10483p  
N | KLLA0F18040p  
O | 40S ribosomal protein S14  
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  
e | 40S ribosomal protein S30  
h | 60S ribosomal protein L41-A  
i | Eukaryotic translation initiation factor 1A  
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_X.mrc

Opened 0057_6gsm_X.mrc as #2, grid size 88,88,112, pixel 1, shown at level
0.153, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_X.cif (#1) to map 0057_6gsm_X.mrc (#2) using 24244
atoms  
average map value = 0.08409, steps = 40  
shifted from previous position = 0.373  
rotated from previous position = 0.099 degrees  
atoms outside contour = 23533, contour level = 0.15287  
  
Position of 0057_6gsm_X.cif (#1) relative to 0057_6gsm_X.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999908 0.00000025 0.00135501 -0.57857011  
-0.00000170 0.99999943 0.00107085 -0.40116203  
-0.00135501 -0.00107086 0.99999851 0.45634782  
Axis -0.62003964 0.78457028 -0.00056271  
Axis point 336.35507218 0.00000000 407.19792982  
Rotation angle (degrees) 0.09895421  
Shift along axis 0.04373981  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X_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 192,109,163,319,204,242

> 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 18608 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 49791  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
49792  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
49793  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
49794  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
49795  
111 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
50044  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
50045  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
50046  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
50047  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
50048  
131 messages similar to the above omitted  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:577  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:577  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:577  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:910  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1012  
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1181  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1270  
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1270  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1286  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1286  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1287  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1287  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1306  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1308  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1308  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1435  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1436  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1526  
Atom C4' has no neighbors to form bonds with according to residue template for
U /2:1556  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1556  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1589  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1592  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1596  
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:1596  
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1602  
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1784  
Atom CD has no neighbors to form bonds with according to residue template for
LYS /C:93  
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /C:93  
Atom N has no neighbors to form bonds with according to residue template for
ARG /D:143  
Atom C has no neighbors to form bonds with according to residue template for
ARG /D:143  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /F:55  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /F:94  
Atom N has no neighbors to form bonds with according to residue template for
ASN /F:130  
Atom N has no neighbors to form bonds with according to residue template for
LEU /F:132  
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /F:133  
Atom N 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
THR /O:93  
Atom CB has no neighbors to form bonds with according to residue template for
VAL /S:52  
Atom O has no neighbors to form bonds with according to residue template for
LEU /S:66  
Atom N has no neighbors to form bonds with according to residue template for
ALA /S:83  
Atom CE3 has no neighbors to form bonds with according to residue template for
TRP /S:84  
Atom CD1 has no neighbors to form bonds with according to residue template for
PHE /S:128  
Atom CB has no neighbors to form bonds with according to residue template for
PRO /T:31  
Atom N has no neighbors to form bonds with according to residue template for
PHE /T:54  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /Z:49  
Atom CD has no neighbors to form bonds with according to residue template for
ARG /Z:49  
Atom O has no neighbors to form bonds with according to residue template for
GLU /Z:84  
Atom N has no neighbors to form bonds with according to residue template for
VAL /Z:92  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /Z:92  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /a:89  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /c:31  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /c:34  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /c:34  
Atom N has no neighbors to form bonds with according to residue template for
TYR /i:28  
Atom N has no neighbors to form bonds with according to residue template for
GLU /i:30  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /i:30  
Atom O has no neighbors to form bonds with according to residue template for
SER /i:50  
Atom N has no neighbors to form bonds with according to residue template for
GLN /k:175  
Atom N has no neighbors to form bonds with according to residue template for
LEU /k:260  
Atom N has no neighbors to form bonds with according to residue template for
MET /k:310  
Atom N has no neighbors to form bonds with according to residue template for
GLU /k:457  
Atom N has no neighbors to form bonds with according to residue template for
ALA /k:477  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /l:131  
Atom ND1 has no neighbors to form bonds with according to residue template for
HIS /p:145  
Atom O has no neighbors to form bonds with according to residue template for
LEU /p:149  
Atom O has no neighbors to form bonds with according to residue template for
ASP /q:97  
  
Chain information for 0057_6gsm_1.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
D | KLLA0D08305p  
F | KLLA0D10659p  
O | 40S ribosomal protein S14  
P | KLLA0F07843p  
Q | 40S ribosomal protein S16  
S | KLLA0B01562p  
T | KLLA0A07194p  
U | KLLA0F25542p  
Z | KLLA0B06182p  
a | 40S ribosomal protein S26  
c | 40S ribosomal protein S28  
d | 40S ribosomal protein S29  
i | Eukaryotic translation initiation factor 1A  
j | Eukaryotic translation initiation factor 2 subunit alpha  
k | Eukaryotic translation initiation factor 2 subunit gamma  
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_1.mrc

Opened 0057_6gsm_1.mrc as #2, grid size 128,96,80, pixel 1, shown at level
0.126, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_1.cif (#1) to map 0057_6gsm_1.mrc (#2) using 18608
atoms  
average map value = 0.0684, steps = 64  
shifted from previous position = 0.53  
rotated from previous position = 0.158 degrees  
atoms outside contour = 17745, contour level = 0.126  
  
Position of 0057_6gsm_1.cif (#1) relative to 0057_6gsm_1.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999827 0.00173579 0.00066214 -0.84382811  
-0.00173443 0.99999640 -0.00204519 0.72064419  
-0.00066568 0.00204403 0.99999769 -0.47427235  
Axis 0.74010988 0.24032262 -0.62807835  
Axis point 0.00000000 279.59960222 369.90215785  
Rotation angle (degrees) 0.15828409  
Shift along axis -0.15345823  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1_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 164,80,175,251,151,246

> 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 6379 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 37310  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
37311  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
37312  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
37313  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
37314  
197 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
37563  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
37564  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
37565  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
37566  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
37567  
227 messages similar to the above omitted  
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:43  
Atom O3' has no neighbors to form bonds with according to residue template for
A /1:44  
Atom O3' has no neighbors to form bonds with according to residue template for
H2U /1:47  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1166  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1169  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1348  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1357  
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:1357  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1358  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1364  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1365  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1367  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1377  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1465  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1483  
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1542  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1564  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /F:62  
Atom N has no neighbors to form bonds with according to residue template for
ARG /F:145  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /Q:28  
Atom O has no neighbors to form bonds with according to residue template for
ASP /Q:120  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /S:41  
Atom N has no neighbors to form bonds with according to residue template for
ARG /S:68  
Atom N has no neighbors to form bonds with according to residue template for
VAL /S:70  
Atom N has no neighbors to form bonds with according to residue template for
ARG /S:143  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /T:34  
Atom N has no neighbors to form bonds with according to residue template for
THR /T:39  
Atom N has no neighbors to form bonds with according to residue template for
GLN /T:70  
Atom O has no neighbors to form bonds with according to residue template for
GLN /T:70  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /T:76  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /T:95  
Atom N has no neighbors to form bonds with according to residue template for
VAL /T:114  
Atom OG has no neighbors to form bonds with according to residue template for
SER /T:125  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /c:53  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /c:53  
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:27  
Atom O has no neighbors to form bonds with according to residue template for
ILE /j:27  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /j:67  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /j:73  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /j:73  
Atom O has no neighbors to form bonds with according to residue template for
ASP /j:84  
  
Chain information for 0057_6gsm_Z.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
F | KLLA0D10659p  
Q | 40S ribosomal protein S16  
S | KLLA0B01562p  
T | KLLA0A07194p  
Z | KLLA0B06182p  
c | 40S ribosomal protein S28  
j | Eukaryotic translation initiation factor 2 subunit alpha  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z.mrc

Opened 0057_6gsm_Z.mrc as #2, grid size 88,72,72, pixel 1, shown at level
0.12, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_Z.cif (#1) to map 0057_6gsm_Z.mrc (#2) using 6379 atoms  
average map value = 0.07059, steps = 52  
shifted from previous position = 0.758  
rotated from previous position = 0.382 degrees  
atoms outside contour = 6034, contour level = 0.1198  
  
Position of 0057_6gsm_Z.cif (#1) relative to 0057_6gsm_Z.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999732 -0.00041871 0.00227831 -0.60321734  
0.00043294 0.99998038 -0.00624984 1.37470602  
-0.00227564 0.00625081 0.99997787 -1.05746611  
Axis 0.93767464 0.34159226 0.06388265  
Axis point 0.00000000 168.30919662 228.37113330  
Rotation angle (degrees) 0.38192337  
Shift along axis -0.16358642  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z_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 136,215,208,223,310,311

> 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 14921 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H.cif  
---  
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 46024  
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
46025  
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
46026  
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
46027  
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
46028  
132 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 46281  
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 46282  
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 46283  
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 46284  
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 46285  
179 messages similar to the above omitted  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:14  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:14  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:15  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:213  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:307  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:370  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:370  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:371  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:372  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:628  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:718  
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:728  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:793  
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:840  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:841  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:877  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:877  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:935  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:941  
Atom C1' has no neighbors to form bonds with according to residue template for
C /2:942  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:947  
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:947  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1060  
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1296  
Atom O has no neighbors to form bonds with according to residue template for
ILE /A:133  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /A:133  
Atom N has no neighbors to form bonds with according to residue template for
ALA /A:145  
Atom O has no neighbors to form bonds with according to residue template for
ALA /A:145  
Atom CA has no neighbors to form bonds with according to residue template for
VAL /A:181  
Atom O has no neighbors to form bonds with according to residue template for
VAL /A:181  
Atom NE has no neighbors to form bonds with according to residue template for
ARG /A:185  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /C:173  
Atom O has no neighbors to form bonds with according to residue template for
VAL /C:221  
Atom N has no neighbors to form bonds with according to residue template for
TYR /C:251  
Atom C has no neighbors to form bonds with according to residue template for
TYR /C:251  
Atom N has no neighbors to form bonds with according to residue template for
ARG /E:233  
Atom CB has no neighbors to form bonds with according to residue template for
ARG /E:233  
Atom N has no neighbors to form bonds with according to residue template for
LYS /L:46  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /L:125  
Atom CG has no neighbors to form bonds with according to residue template for
GLU /V:2  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /V:2  
Atom C has no neighbors to form bonds with according to residue template for
ALA /X:25  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /X:25  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /a:15  
Atom O has no neighbors to form bonds with according to residue template for
PHE /q:254  
Atom O has no neighbors to form bonds with according to residue template for
PHE /q:255  
Atom O has no neighbors to form bonds with according to residue template for
VAL /q:270  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /q:281  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /q:287  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /q:303  
Atom N has no neighbors to form bonds with according to residue template for
GLN /q:334  
Atom CB has no neighbors to form bonds with according to residue template for
GLN /q:334  
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /q:334  
Atom N has no neighbors to form bonds with according to residue template for
THR /q:335  
Atom N has no neighbors to form bonds with according to residue template for
LYS /q:443  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /q:443  
Atom CE has no neighbors to form bonds with according to residue template for
LYS /q:443  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /q:486  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /q:488  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /q:560  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /q:576  
Atom N has no neighbors to form bonds with according to residue template for
GLN /q:583  
Atom O has no neighbors to form bonds with according to residue template for
SER /q:592  
Atom OG has no neighbors to form bonds with according to residue template for
SER /q:592  
Atom CA has no neighbors to form bonds with according to residue template for
SER /q:593  
Atom OG has no neighbors to form bonds with according to residue template for
SER /q:593  
Atom N has no neighbors to form bonds with according to residue template for
THR /q:634  
Atom C has no neighbors to form bonds with according to residue template for
THR /q:634  
Atom N has no neighbors to form bonds with according to residue template for
ARG /q:654  
  
Chain information for 0057_6gsm_H.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  
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_H.mrc

Opened 0057_6gsm_H.mrc as #2, grid size 88,96,104, pixel 1, shown at level
0.137, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_H.cif (#1) to map 0057_6gsm_H.mrc (#2) using 14921
atoms  
average map value = 0.07261, steps = 80  
shifted from previous position = 0.499  
rotated from previous position = 0.179 degrees  
atoms outside contour = 14137, contour level = 0.1369  
  
Position of 0057_6gsm_H.cif (#1) relative to 0057_6gsm_H.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999531 -0.00126111 -0.00279203 0.90794240  
0.00125934 0.99999900 -0.00063652 -0.43925796  
0.00279283 0.00063300 0.99999590 -1.02865610  
Axis 0.20288211 -0.89252153 0.40279544  
Axis point 392.13097233 0.00000000 312.76567637  
Rotation angle (degrees) 0.17926176  
Shift along axis 0.16191447  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H_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 208,140,133,327,211,220

> 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 11892 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_l.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_l.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_l.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_l.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 42944  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
42945  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
42946  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
42947  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
42948  
140 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
43197  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
43198  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
43199  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
43200  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
43201  
168 messages similar to the above omitted  
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:19  
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:562  
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:562  
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1003  
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:1151  
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1191  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1193  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1193  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1207  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1217  
Atom N1 has no neighbors to form bonds with according to residue template for
G /2:1217  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1217  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1243  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1269  
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1273  
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:1273  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1425  
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1446  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1540  
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:1542  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1553  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1553  
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1554  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1554  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1567  
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1577  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1617  
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1626  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1626  
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1768  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1776  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1790  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1790  
Atom C1' has no neighbors to form bonds with according to residue template for
G /2:1790  
Atom N has no neighbors to form bonds with according to residue template for
GLU /F:183  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /F:218  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /F:218  
Atom C has no neighbors to form bonds with according to residue template for
LYS /P:59  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /P:64  
Atom CE has no neighbors to form bonds with according to residue template for
LYS /P:64  
Atom N has no neighbors to form bonds with according to residue template for
VAL /P:86  
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /P:86  
Atom O has no neighbors to form bonds with according to residue template for
PRO /a:2  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /i:90  
Atom O has no neighbors to form bonds with according to residue template for
LYS /j:35  
Atom O has no neighbors to form bonds with according to residue template for
ILE /j:46  
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /j:46  
Atom O has no neighbors to form bonds with according to residue template for
ILE /j:95  
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /j:96  
Atom O has no neighbors to form bonds with according to residue template for
LYS /j:106  
Atom SG has no neighbors to form bonds with according to residue template for
CYS /j:262  
Atom N has no neighbors to form bonds with according to residue template for
ASN /j:263  
Atom O has no neighbors to form bonds with according to residue template for
LYS /p:142  
Atom CG has no neighbors to form bonds with according to residue template for
GLU /p:290  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /p:290  
Atom N has no neighbors to form bonds with according to residue template for
ILE /p:292  
Atom N has no neighbors to form bonds with according to residue template for
HIS /p:310  
Atom CE1 has no neighbors to form bonds with according to residue template for
HIS /p:310  
  
Chain information for 0057_6gsm_l.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
3 | mRNA (5'-R(P*AP*AP*U)-3')  
F | KLLA0D10659p  
P | KLLA0F07843p  
Q | 40S ribosomal protein S16  
S | KLLA0B01562p  
c | 40S ribosomal protein S28  
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  
k | Eukaryotic translation initiation factor 2 subunit gamma  
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_l.mrc

Opened 0057_6gsm_l.mrc as #2, grid size 120,72,88, pixel 1, shown at level
0.117, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_l.cif (#1) to map 0057_6gsm_l.mrc (#2) using 11892
atoms  
average map value = 0.06384, steps = 72  
shifted from previous position = 0.608  
rotated from previous position = 0.153 degrees  
atoms outside contour = 11222, contour level = 0.11707  
  
Position of 0057_6gsm_l.cif (#1) relative to 0057_6gsm_l.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999771 0.00015409 0.00213271 -0.96507720  
-0.00015068 0.99999871 -0.00159690 0.08959189  
-0.00213295 0.00159657 0.99999645 0.13446134  
Axis 0.59832829 0.79921371 -0.05710259  
Axis point 48.77929787 0.00000000 308.50125021  
Rotation angle (degrees) 0.15290296  
Shift along axis -0.51350801  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_l_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 169,131,65,248,202,184

> 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 10038 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_f.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_f.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_f.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_f.cif  
---  
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 41078  
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
41079  
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
41080  
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
41081  
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
41082  
193 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
41331  
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
41332  
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
41333  
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
41334  
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
41335  
220 messages similar to the above omitted  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1193  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1280  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1424  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1464  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1465  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1483  
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1496  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1502  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1588  
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:1603  
Atom O has no neighbors to form bonds with according to residue template for
VAL /D:37  
Atom O has no neighbors to form bonds with according to residue template for
ASP /D:57  
Atom O has no neighbors to form bonds with according to residue template for
ARG /D:64  
Atom N has no neighbors to form bonds with according to residue template for
SER /D:129  
Atom CB has no neighbors to form bonds with according to residue template for
SER /D:129  
Atom O has no neighbors to form bonds with according to residue template for
LYS /D:190  
Atom CG has no neighbors to form bonds with according to residue template for
LYS /D:190  
Atom N has no neighbors to form bonds with according to residue template for
GLN /M:122  
Atom C has no neighbors to form bonds with according to residue template for
GLN /M:122  
Atom CB has no neighbors to form bonds with according to residue template for
GLN /M:122  
Atom N has no neighbors to form bonds with according to residue template for
MET /P:28  
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /S:110  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /T:41  
Atom N has no neighbors to form bonds with according to residue template for
TYR /T:80  
Atom N has no neighbors to form bonds with according to residue template for
ALA /T:96  
Atom O has no neighbors to form bonds with according to residue template for
ALA /T:96  
Atom O has no neighbors to form bonds with according to residue template for
THR /U:29  
Atom N has no neighbors to form bonds with according to residue template for
ARG /d:56  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /i:65  
Atom N has no neighbors to form bonds with according to residue template for
LEU /i:78  
Atom CB has no neighbors to form bonds with according to residue template for
LEU /i:78  
Atom N has no neighbors to form bonds with according to residue template for
LEU /i:109  
Atom O has no neighbors to form bonds with according to residue template for
ARG /l:167  
Atom N has no neighbors to form bonds with according to residue template for
GLN /l:178  
Atom CB has no neighbors to form bonds with according to residue template for
GLN /l:178  
Atom N has no neighbors to form bonds with according to residue template for
ASP /l:179  
  
Chain information for 0057_6gsm_f.cif #1  
---  
Chain | Description  
1 | Met-tRNAi  
2 | 18S ribosomal RNA  
D | KLLA0D08305p  
K | KLLA0B08173p  
M | 40S ribosomal protein S12  
P | KLLA0F07843p  
S | KLLA0B01562p  
T | KLLA0A07194p  
U | KLLA0F25542p  
d | 40S ribosomal protein S29  
f | Ubiquitin-40S ribosomal protein S27a  
i | Eukaryotic translation initiation factor 1A  
l | Eukaryotic translation initiation factor 2 subunit beta  
  

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_f.mrc

Opened 0057_6gsm_f.mrc as #2, grid size 80,72,120, pixel 1, shown at level
0.121, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_f.cif (#1) to map 0057_6gsm_f.mrc (#2) using 10038
atoms  
average map value = 0.07064, steps = 48  
shifted from previous position = 0.453  
rotated from previous position = 0.191 degrees  
atoms outside contour = 9477, contour level = 0.12053  
  
Position of 0057_6gsm_f.cif (#1) relative to 0057_6gsm_f.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999742 0.00017353 -0.00226392 0.00548192  
-0.00016801 0.99999701 0.00243768 -0.65676907  
0.00226434 -0.00243729 0.99999447 0.03413541  
Axis -0.73171784 -0.67967718 -0.05126334  
Axis point 0.00000000 22.94036133 146.59506449  
Rotation angle (degrees) 0.19086294  
Shift along axis 0.44062983  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_f_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 129,148,171,200,243,290

> 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 16133 atoms in map 0057_6gsm_Sampled.mrc #2 bounds  

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_R.cif
> #1 selectedOnly true

> save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_R.mrc
> #2

> close #1

> close #2

> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_R.cif

Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_R.cif  
---  
warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
near line 47208  
Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
47209  
Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
47210  
Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
47211  
Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
47212  
88 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
line 47466  
Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
line 47467  
Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
line 47468  
Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
line 47469  
Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
line 47470  
155 messages similar to the above omitted  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:2  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:2  
Atom O3' 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
U /2:12  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:13  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:591  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:591  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:955  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1034  
Atom O2' 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
C /2:1044  
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1047  
Atom OP2 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
A /2:1064  
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1085  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1087  
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1099  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1142  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1142  
Atom O2' 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 /2:1152  
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:1159  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1162  
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1163  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1163  
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:1198  
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1200  
Atom C4 has no neighbors to form bonds with according to residue template for
G /2:1200  
Atom N1 has no neighbors to form bonds with according to residue template for
G /2:1272  
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1272  
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1276  
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:1375  
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1377  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1424  
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1513  
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1513  
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1600  
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1616  
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:1616  
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1621  
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1621  
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1797  
Atom CB has no neighbors to form bonds with according to residue template for
LYS /B:202  
Atom C has no neighbors to form bonds with according to residue template for
ARG /C:96  
Atom N has no neighbors to form bonds with according to residue template for
THR /C:231  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /C:231  
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /C:231  
Atom N has no neighbors to form bonds with according to residue template for
ARG /D:94  
Atom C has no neighbors to form bonds with according to residue template for
ARG /D:94  
Atom NE has no neighbors to form bonds with according to residue template for
ARG /D:94  
Atom CB has no neighbors to form bonds with according to residue template for
ALA /D:114  
Atom N has no neighbors to form bonds with according to residue template for
SER /D:221  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /F:60  
Atom N has no neighbors to form bonds with according to residue template for
CYS /F:89  
Atom SG has no neighbors to form bonds with according to residue template for
CYS /F:89  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /J:33  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /J:33  
Atom N has no neighbors to form bonds with according to residue template for
HIS /N:58  
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 N has no neighbors to form bonds with according to residue template for
PHE /Q:138  
Atom O has no neighbors to form bonds with according to residue template for
LEU /U:26  
Atom N has no neighbors to form bonds with according to residue template for
PHE /U:48  
Atom C has no neighbors to form bonds with according to residue template for
PHE /U:48  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /W:66  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /W:69  
Atom N has no neighbors to form bonds with according to residue template for
CYS /W:72  
Atom O has no neighbors to form bonds with according to residue template for
CYS /W:72  
Atom O has no neighbors to form bonds with according to residue template for
CYS /b:40  
Atom SG has no neighbors to form bonds with according to residue template for
CYS /b:40  
Atom O has no neighbors to form bonds with according to residue template for
VAL /b:54  
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /b:62  
Atom N has no neighbors to form bonds with according to residue template for
THR /b:65  
Atom O has no neighbors to form bonds with according to residue template for
THR /b:65  
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /b:65  
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /c:40  
Atom O has no neighbors to form bonds with according to residue template for
VAL /c:44  
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /d:49  
Atom CE has no neighbors to form bonds with according to residue template for
MET /e:56  
Atom N has no neighbors to form bonds with according to residue template for
ASN /g:79  
Atom C has no neighbors to form bonds with according to residue template for
ASN /g:79  
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /g:101  
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /g:117  
Atom N has no neighbors to form bonds with according to residue template for
TRP /g:186  
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /g:188  
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /g:188  
Atom O has no neighbors to form bonds with according to residue template for
TYR /g:193  
Atom N has no neighbors to form bonds with according to residue template for
PHE /g:238  
Atom N has no neighbors to form bonds with according to residue template for
GLU /o:9  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /o:9  
Atom O has no neighbors to form bonds with according to residue template for
ALA /o:15  
Atom N has no neighbors to form bonds with according to residue template for
GLU /o:61  
Atom C has no neighbors to form bonds with according to residue template for
GLU /o:61  
Atom O has no neighbors to form bonds with according to residue template for
ARG /o:156  
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /o:201  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /o:257  
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /q:309  
Atom N has no neighbors to form bonds with according to residue template for
GLN /q:604  
  
Chain information for 0057_6gsm_R.cif #1  
---  
Chain | Description  
2 | 18S ribosomal RNA  
A | 40S ribosomal protein S0  
B | 40S ribosomal protein S1  
C | KLLA0F09812p  
D | KLLA0D08305p  
F | KLLA0D10659p  
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  
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  
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_R.mrc

Opened 0057_6gsm_R.mrc as #2, grid size 72,96,120, pixel 1, shown at level
0.129, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule 0057_6gsm_R.cif (#1) to map 0057_6gsm_R.mrc (#2) using 16133
atoms  
average map value = 0.06832, steps = 40  
shifted from previous position = 0.394  
rotated from previous position = 0.046 degrees  
atoms outside contour = 15398, contour level = 0.12946  
  
Position of 0057_6gsm_R.cif (#1) relative to 0057_6gsm_R.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999986 0.00050653 0.00015865 -0.10325212  
-0.00050643 0.99999969 -0.00060125 -0.02149171  
-0.00015896 0.00060117 0.99999981 -0.39826988  
Axis 0.74964305 0.19801208 -0.63152713  
Axis point 0.00000000 484.02758995 -91.93522150  
Rotation angle (degrees) 0.04595060  
Shift along axis 0.16986038  
  

> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_R_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 118,200,179,205,279,266

> 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

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