"chains" that are not polymers

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.93 (2020-04-03)
Description
This is a pretty obscure case, and perhaps more a case of user error than a bug... but I'm working on a model passed to me where multiple chains have a free valine residue bound as a ligand. The original modeller has chosen to put all these in their own chain, with consecutive numbering... I'm sure you can see where this is going. Makes for a rather comical-looking cartoon!

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6u42

Summary of feedback from opening 6u42 fetched from pdb  
---  
note |  
  
  
| Summary of feedback from opening /home/tic20/Downloads/ChimeraX/PDB/6u42.cif  
  
---  
  
  
  
  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 1385337  
  
  
  
  
  
6u42 title:  
Natively decorated ciliary doublet microtubule [more info...]  
  
Chain information for 6u42 #1  
---  
Chain | Description  
0A 0C 0E 0G 0I 0K 0M 0O 0Q 0S 0U 0W 0Y 1 1A 1C 1E 1G 1K 1M 1O 1Q 1S 1U 1W 2A
2C 2E 2G 2I 2K 2M 2Q 2S 2U 2W 2Y 3 3A 3C 3G 3I 3K 3M 3O 3Q 3S 5 7 9 A1 A3 A5
A7 A9 B1 B3 B5 B8 C0 C2 C4 C6 C8 D0 D2 D4 D6 D8 E0 E2 E4 E6 E8 F0 F2 F6 F8 G0
G2 G4 G6 G8 H2 H4 H6 H8 I0 I2 I4 I8 J0 J2 J4 J6 J8 K0 K4 K6 K8 L0 L2 L4 L6 M0
M2 M4 M6 M8 N0 N2 N6 N8 O0 O2 O4 O6 O8 P4 P6 P8 Q0 Q2 Q4 Q6 Q8 R0 R2 R4 R6 R8
S0 S2 S4 S6 S8 T0 T2 T4 T6 T8 U2 U4 U6 U8 V0 V2 V4 V6 V8 W0 W2 W4 W6 W8 X0 X2
X4 X6 X8 Y0 Y2 Y4 Y6 Y8 Z0 Z2 Z4 Z6 Z8 | Tubulin β  
0B 0F 0H 0J 0L 0N 0P 0R 0V 0X 0Z 1B 1D 1F 1H 1L 1N 1P 1R 1T 1V 1X 1Z 2 2B 2D
2F 2H 2J 2L 2N 2P 2R 2T 2V 2X 2Z 3B 3D 3F 3H 3J 3L 3N 3P 3R 3T 4 6 8 A0 A2 A4
A8 B0 B2 B4 B7 B9 C1 C5 C7 C9 D1 D3 D5 D7 E1 E3 E5 E7 E9 F1 F3 F5 F7 F9 G1 G3
G5 G7 G9 H1 H3 H5 H7 H9 I1 I3 I5 I7 I9 J1 J3 J5 J7 J9 K1 K3 K5 K7 K9 L1 L3 L5
L7 L9 M1 M3 M5 M7 M9 N1 N3 N5 N7 N9 O1 O3 O5 O7 O9 P3 P5 P7 P9 Q1 Q3 Q5 Q9 R1
R3 R5 R7 R9 S1 S5 S7 S9 T1 T3 T5 T7 U1 U3 U5 U7 U9 V1 V3 V7 V9 W1 W3 W5 W7 W9
X3 X5 X7 X9 Y1 Y3 Y5 Y9 Z1 Z3 Z5 Z7 Z9 | Tubulin α  
3V 3X 3Z 4B 4D 4F 4H 4J | PACRG  
3W 3Y 4A 4C 4E 4G 4I | FAP20  
4L 4M | FAP53  
4N 4O 4P | FAP127  
4Q 4R 4S 4T 4U | RIB43a  
4V 4W 4X | FAP112  
4Y 4Z | FAP210  
5A 5B 5C 5D | FAP45  
5E | RIB30  
5F 5G 7B | FAP363  
5H 5I 5J 5K | FAP126  
5L 5M 5N | FAP52  
5O 5P | FAP67  
5Q | FAP85  
5R 5S 5T 5U 5V | FAP106  
5X 5Y 5Z 6A 6B 6C 6D | FAP115  
6E | FAP143  
6F | FAP161  
6G 6H | FAP166  
6I 6J 6K 6L 6M 6N 6O 6P | FAP252  
6Q 6R 6S | FAP276  
6T 6U 6V 6W 6X 6Y 6Z 7A | RIB72  
7C | FAP141  
7D 7E 7F | FAP222  
7G | FAP95  
7H 7X | FAP182  
7I 7J | FAP129  
7K 7L | FAP21  
7M 7N | FAP273  
7O 7P | FAP107  
7Q | RIB21  
7R 7S | DC1  
7T 7U | DC2  
7V 7W | DC3  
7Y | FAP68  
7Z 8A 8B 8C 8D | FAP90  
  
Non-standard residues in 6u42 #1  
---  
MG — magnesium ion  
  
  

> open 20631 fromDatabase emdb

Opened emd_20631.map, grid size 512,512,512, pixel 1.4, shown at level 0.0352,
step 2, values float32  

> clipper associate #2 toModel #1

6u42 title:  
Natively decorated ciliary doublet microtubule [more info...]  
  
Chain information for 6u42  
---  
Chain | Description  
1.2/0A 1.2/0C 1.2/0E 1.2/0G 1.2/0I 1.2/0K 1.2/0M 1.2/0O 1.2/0Q 1.2/0S 1.2/0U
1.2/0W 1.2/0Y 1.2/1 1.2/1A 1.2/1C 1.2/1E 1.2/1G 1.2/1K 1.2/1M 1.2/1O 1.2/1Q
1.2/1S 1.2/1U 1.2/1W 1.2/2A 1.2/2C 1.2/2E 1.2/2G 1.2/2I 1.2/2K 1.2/2M 1.2/2Q
1.2/2S 1.2/2U 1.2/2W 1.2/2Y 1.2/3 1.2/3A 1.2/3C 1.2/3G 1.2/3I 1.2/3K 1.2/3M
1.2/3O 1.2/3Q 1.2/3S 1.2/5 1.2/7 1.2/9 1.2/A1 1.2/A3 1.2/A5 1.2/A7 1.2/A9
1.2/B1 1.2/B3 1.2/B5 1.2/B8 1.2/C0 1.2/C2 1.2/C4 1.2/C6 1.2/C8 1.2/D0 1.2/D2
1.2/D4 1.2/D6 1.2/D8 1.2/E0 1.2/E2 1.2/E4 1.2/E6 1.2/E8 1.2/F0 1.2/F2 1.2/F6
1.2/F8 1.2/G0 1.2/G2 1.2/G4 1.2/G6 1.2/G8 1.2/H2 1.2/H4 1.2/H6 1.2/H8 1.2/I0
1.2/I2 1.2/I4 1.2/I8 1.2/J0 1.2/J2 1.2/J4 1.2/J6 1.2/J8 1.2/K0 1.2/K4 1.2/K6
1.2/K8 1.2/L0 1.2/L2 1.2/L4 1.2/L6 1.2/M0 1.2/M2 1.2/M4 1.2/M6 1.2/M8 1.2/N0
1.2/N2 1.2/N6 1.2/N8 1.2/O0 1.2/O2 1.2/O4 1.2/O6 1.2/O8 1.2/P4 1.2/P6 1.2/P8
1.2/Q0 1.2/Q2 1.2/Q4 1.2/Q6 1.2/Q8 1.2/R0 1.2/R2 1.2/R4 1.2/R6 1.2/R8 1.2/S0
1.2/S2 1.2/S4 1.2/S6 1.2/S8 1.2/T0 1.2/T2 1.2/T4 1.2/T6 1.2/T8 1.2/U2 1.2/U4
1.2/U6 1.2/U8 1.2/V0 1.2/V2 1.2/V4 1.2/V6 1.2/V8 1.2/W0 1.2/W2 1.2/W4 1.2/W6
1.2/W8 1.2/X0 1.2/X2 1.2/X4 1.2/X6 1.2/X8 1.2/Y0 1.2/Y2 1.2/Y4 1.2/Y6 1.2/Y8
1.2/Z0 1.2/Z2 1.2/Z4 1.2/Z6 1.2/Z8 | Tubulin β  
1.2/0B 1.2/0F 1.2/0H 1.2/0J 1.2/0L 1.2/0N 1.2/0P 1.2/0R 1.2/0V 1.2/0X 1.2/0Z
1.2/1B 1.2/1D 1.2/1F 1.2/1H 1.2/1L 1.2/1N 1.2/1P 1.2/1R 1.2/1T 1.2/1V 1.2/1X
1.2/1Z 1.2/2 1.2/2B 1.2/2D 1.2/2F 1.2/2H 1.2/2J 1.2/2L 1.2/2N 1.2/2P 1.2/2R
1.2/2T 1.2/2V 1.2/2X 1.2/2Z 1.2/3B 1.2/3D 1.2/3F 1.2/3H 1.2/3J 1.2/3L 1.2/3N
1.2/3P 1.2/3R 1.2/3T 1.2/4 1.2/6 1.2/8 1.2/A0 1.2/A2 1.2/A4 1.2/A8 1.2/B0
1.2/B2 1.2/B4 1.2/B7 1.2/B9 1.2/C1 1.2/C5 1.2/C7 1.2/C9 1.2/D1 1.2/D3 1.2/D5
1.2/D7 1.2/E1 1.2/E3 1.2/E5 1.2/E7 1.2/E9 1.2/F1 1.2/F3 1.2/F5 1.2/F7 1.2/F9
1.2/G1 1.2/G3 1.2/G5 1.2/G7 1.2/G9 1.2/H1 1.2/H3 1.2/H5 1.2/H7 1.2/H9 1.2/I1
1.2/I3 1.2/I5 1.2/I7 1.2/I9 1.2/J1 1.2/J3 1.2/J5 1.2/J7 1.2/J9 1.2/K1 1.2/K3
1.2/K5 1.2/K7 1.2/K9 1.2/L1 1.2/L3 1.2/L5 1.2/L7 1.2/L9 1.2/M1 1.2/M3 1.2/M5
1.2/M7 1.2/M9 1.2/N1 1.2/N3 1.2/N5 1.2/N7 1.2/N9 1.2/O1 1.2/O3 1.2/O5 1.2/O7
1.2/O9 1.2/P3 1.2/P5 1.2/P7 1.2/P9 1.2/Q1 1.2/Q3 1.2/Q5 1.2/Q9 1.2/R1 1.2/R3
1.2/R5 1.2/R7 1.2/R9 1.2/S1 1.2/S5 1.2/S7 1.2/S9 1.2/T1 1.2/T3 1.2/T5 1.2/T7
1.2/U1 1.2/U3 1.2/U5 1.2/U7 1.2/U9 1.2/V1 1.2/V3 1.2/V7 1.2/V9 1.2/W1 1.2/W3
1.2/W5 1.2/W7 1.2/W9 1.2/X3 1.2/X5 1.2/X7 1.2/X9 1.2/Y1 1.2/Y3 1.2/Y5 1.2/Y9
1.2/Z1 1.2/Z3 1.2/Z5 1.2/Z7 1.2/Z9 | Tubulin α  
1.2/3V 1.2/3X 1.2/3Z 1.2/4B 1.2/4D 1.2/4F 1.2/4H 1.2/4J | PACRG  
1.2/3W 1.2/3Y 1.2/4A 1.2/4C 1.2/4E 1.2/4G 1.2/4I | FAP20  
1.2/4L 1.2/4M | FAP53  
1.2/4N 1.2/4O 1.2/4P | FAP127  
1.2/4Q 1.2/4R 1.2/4S 1.2/4T 1.2/4U | RIB43a  
1.2/4V 1.2/4W 1.2/4X | FAP112  
1.2/4Y 1.2/4Z | FAP210  
1.2/5A 1.2/5B 1.2/5C 1.2/5D | FAP45  
1.2/5E | RIB30  
1.2/5F 1.2/5G 1.2/7B | FAP363  
1.2/5H 1.2/5I 1.2/5J 1.2/5K | FAP126  
1.2/5L 1.2/5M 1.2/5N | FAP52  
1.2/5O 1.2/5P | FAP67  
1.2/5Q | FAP85  
1.2/5R 1.2/5S 1.2/5T 1.2/5U 1.2/5V | FAP106  
1.2/5X 1.2/5Y 1.2/5Z 1.2/6A 1.2/6B 1.2/6C 1.2/6D | FAP115  
1.2/6E | FAP143  
1.2/6F | FAP161  
1.2/6G 1.2/6H | FAP166  
1.2/6I 1.2/6J 1.2/6K 1.2/6L 1.2/6M 1.2/6N 1.2/6O 1.2/6P | FAP252  
1.2/6Q 1.2/6R 1.2/6S | FAP276  
1.2/6T 1.2/6U 1.2/6V 1.2/6W 1.2/6X 1.2/6Y 1.2/6Z 1.2/7A | RIB72  
1.2/7C | FAP141  
1.2/7D 1.2/7E 1.2/7F | FAP222  
1.2/7G | FAP95  
1.2/7H 1.2/7X | FAP182  
1.2/7I 1.2/7J | FAP129  
1.2/7K 1.2/7L | FAP21  
1.2/7M 1.2/7N | FAP273  
1.2/7O 1.2/7P | FAP107  
1.2/7Q | RIB21  
1.2/7R 1.2/7S | DC1  
1.2/7T 1.2/7U | DC2  
1.2/7V 1.2/7W | DC3  
1.2/7Y | FAP68  
1.2/7Z 1.2/8A 1.2/8B 1.2/8C 1.2/8D | FAP90  
  
Non-standard residues in 6u42 #1.2  
---  
MG — magnesium ion  
  

> toolshed show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> hide #1.3 models

> show #1.3 models

> isolde start

> set selectionWidth 4

Done loading forcefield  

QWidget::repaint: Recursive repaint detected  

> addh

Summary of feedback from adding hydrogens to 6u42 #1.2  
---  
warning | Not adding hydrogens to /3B THR 41 CB because it is missing heavy-
atom bond partners  
notes | Termini for 6u42 (#1.2) chain 1 determined from SEQRES records  
Termini for 6u42 (#1.2) chain 2 determined from SEQRES records  
Termini for 6u42 (#1.2) chain 3 determined from SEQRES records  
Termini for 6u42 (#1.2) chain 4 determined from SEQRES records  
Termini for 6u42 (#1.2) chain 5 determined from SEQRES records  
446 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /3 MET 1, /5 MET 1, /7 MET
1, /9 MET 1, /A1 MET 1, /A3 MET 1, /A5 MET 1, /A7 MET 1, /A9 MET 1, /B1 MET 1,
/B3 MET 1, /B5 MET 1, /B8 MET 1, /C0 MET 1, /C2 MET 1, /C4 MET 1, /C6 MET 1,
/C8 MET 1, /D0 MET 1, /D2 MET 1, /D4 MET 1, /D6 MET 1, /D8 MET 1, /E0 MET 1,
/E2 MET 1, /E4 MET 1, /E6 MET 1, /E8 MET 1, /F0 MET 1, /F2 MET 1, /F6 MET 1,
/F8 MET 1, /G0 MET 1, /G2 MET 1, /G4 MET 1, /G6 MET 1, /G8 MET 1, /H2 MET 1,
/H4 MET 1, /H6 MET 1, /H8 MET 1, /I0 MET 1, /I2 MET 1, /I4 MET 1, /I8 MET 1,
/J0 MET 1, /J2 MET 1, /J4 MET 1, /J6 MET 1, /J8 MET 1, /K0 MET 1, /K4 MET 1,
/K6 MET 1, /K8 MET 1, /L0 MET 1, /L2 MET 1, /L4 MET 1, /L6 MET 1, /M0 MET 1,
/M2 MET 1, /M4 MET 1, /M6 MET 1, /M8 MET 1, /N0 MET 1, /N2 MET 1, /N6 MET 1,
/N8 MET 1, /O0 MET 1, /O2 MET 1, /O4 MET 1, /O6 MET 1, /O8 MET 1, /P4 MET 1,
/P6 MET 1, /P8 MET 1, /Q0 MET 1, /Q2 MET 1, /Q4 MET 1, /Q6 MET 1, /R0 MET 1,
/R2 MET 1, /R4 MET 1, /R6 MET 1, /R8 MET 1, /S0 MET 1, /S2 MET 1, /S4 MET 1,
/S6 MET 1, /S8 MET 1, /T0 MET 1, /T2 MET 1, /T4 MET 1, /T6 MET 1, /T8 MET 1,
/U2 MET 1, /U4 MET 1, /U6 MET 1, /U8 MET 1, /V0 MET 1, /V2 MET 1, /V4 MET 1,
/V6 MET 1, /V8 MET 1, /W0 MET 1, /W2 MET 1, /W4 MET 1, /W6 MET 1, /W8 MET 1,
/X0 MET 1, /X2 MET 1, /X4 MET 1, /X6 MET 1, /X8 MET 1, /Y0 MET 1, /Y2 MET 1,
/Y4 MET 1, /Y6 MET 1, /Y8 MET 1, /Z0 MET 1, /Z2 MET 1, /Z4 MET 1, /Z6 MET 1,
/Z8 MET 1, /0A MET 1, /0C MET 1, /0E MET 1, /0G MET 1, /0I MET 1, /0K MET 1,
/0M MET 1, /0O MET 1, /0Q MET 1, /0S MET 1, /0U MET 1, /0W MET 1, /0Y MET 1,
/1A MET 1, /1C MET 1, /1E MET 1, /1G MET 1, /1K MET 1, /1M MET 1, /1O MET 1,
/1Q MET 1, /1S MET 1, /1U MET 1, /1W MET 1, /2A MET 1, /2C MET 1, /2E MET 1,
/2G MET 1, /2I MET 1, /2K MET 1, /2M MET 1, /2Q MET 1, /2S MET 1, /2U MET 1,
/2W MET 1, /2Y MET 1, /3A MET 1, /3C MET 1, /3G MET 1, /3I MET 1, /3K MET 1,
/3M MET 1, /3O MET 1, /3Q MET 1, /3S MET 1, /3V MET 1, /3W MET 1, /3X MET 1,
/3Y MET 1, /3Z MET 1, /4A MET 1, /4B MET 1, /4C MET 1, /4D MET 1, /4E MET 1,
/4F MET 1, /4G MET 1, /4H MET 1, /4I MET 1, /5E MET 1, /5F MET 1, /6Q MET 1,
/6R MET 1, /6S MET 1, /7B MET 1, /7Z MET 1, /8A MET 1, /8B MET 1, /8C MET 1  
Chain-initial residues that are not actual N termini: /1 LEU 289, /2 ARG 2, /4
ARG 2, /6 ARG 2, /8 ARG 2, /A0 ARG 2, /A2 ARG 2, /A4 ARG 2, /A8 ARG 2, /A8 ASP
47, /B0 ARG 2, /B0 ASP 47, /B2 ARG 2, /B2 ASP 47, /B4 ARG 2, /B4 ASP 47, /B7
ARG 2, /B7 ASP 47, /B9 ARG 2, /B9 ASP 47, /C1 ARG 2, /C1 ASP 47, /C5 ARG 2,
/C7 ARG 2, /C9 ARG 2, /C9 ASP 47, /D1 ARG 2, /D1 ASP 47, /D3 ARG 2, /D3 ASP
47, /D5 ARG 2, /D5 ASP 47, /D7 ARG 2, /D7 ASP 47, /E1 ARG 2, /E1 ASP 47, /E3
ARG 2, /E3 ASP 47, /E5 ARG 2, /E5 ASP 47, /E7 ARG 2, /E7 ASP 47, /E9 ARG 2,
/E9 ASP 47, /F1 ARG 2, /F1 ASP 47, /F3 ARG 2, /F3 ASP 47, /F5 ARG 2, /F5 ASP
47, /F7 ARG 2, /F7 ASP 47, /F9 ARG 2, /G1 ARG 2, /G3 ARG 2, /G5 ARG 2, /G5 ASP
47, /G7 ARG 2, /G7 ASP 47, /G9 ARG 2, /G9 ASP 47, /H1 ARG 2, /H1 ASP 47, /H3
ARG 2, /H3 ASP 47, /H5 ARG 2, /H5 ASP 47, /H7 ARG 2, /H7 ASP 47, /H9 ARG 2,
/H9 ASP 47, /I1 ARG 2, /I1 ASP 47, /I3 ARG 2, /I3 ASP 47, /I5 ARG 2, /I5 ASP
47, /I7 ARG 2, /I7 ASP 47, /I9 ARG 2, /I9 ASP 47, /J1 ARG 2, /J1 ASP 47, /J3
ARG 2, /J3 ASP 46, /J5 ARG 2, /J7 ARG 2, /J7 ASP 47, /J9 ARG 2, /K1 ARG 2, /K1
ASP 47, /K3 ARG 2, /K3 ASP 47, /K5 ARG 2, /K5 ASP 47, /K7 ARG 2, /K7 ASP 47,
/K9 ARG 2, /K9 ASP 47, /L1 ARG 2, /L1 ASP 47, /L3 ARG 2, /L3 ASP 47, /L5 ARG
2, /L5 ASP 47, /L7 ARG 2, /L7 ASP 47, /L9 ARG 2, /L9 ASP 47, /M1 ARG 2, /M1
ASP 47, /M3 ARG 2, /M5 ARG 2, /M5 ASP 47, /M7 ARG 2, /M9 ARG 2, /N1 ARG 2, /N1
ASP 47, /N3 ARG 2, /N3 ASP 47, /N5 ARG 2, /N5 ASP 47, /N7 ARG 2, /N7 ASP 47,
/N9 ARG 2, /N9 ASP 47, /O1 ARG 2, /O1 ASP 47, /O3 ARG 2, /O3 ASP 47, /O5 ARG
2, /O5 ASP 47, /O7 ARG 2, /O7 GLY 44, /O9 ARG 2, /O9 ASP 47, /P3 ARG 2, /P3
ASP 47, /P5 ARG 2, /P7 ARG 2, /P7 ASP 47, /P9 ARG 2, /Q1 ARG 2, /Q1 ASP 47,
/Q3 ARG 2, /Q3 ASP 47, /Q5 ARG 2, /Q5 ASP 47, /Q8 ILE 7, /Q9 ARG 2, /Q9 ASP
47, /R1 ARG 2, /R1 ASP 47, /R3 ARG 2, /R3 ASP 47, /R5 ARG 2, /R7 ARG 2, /R7
ASP 47, /R9 ARG 2, /S1 ARG 2, /S1 ASP 47, /S5 ARG 2, /S5 ASP 47, /S7 ARG 2,
/S9 ARG 2, /S9 ASP 47, /T1 ARG 2, /T1 ASP 47, /T3 ARG 2, /T3 ASP 47, /T5 ARG
2, /T5 ASP 47, /T7 ARG 2, /T7 ASP 47, /U1 ARG 2, /U1 ASP 47, /U3 ARG 2, /U3
ASP 47, /U5 ARG 2, /U5 ASP 47, /U7 ARG 2, /U7 ASP 47, /U9 ARG 2, /U9 ASP 47,
/V1 ARG 2, /V1 ASP 47, /V3 ARG 2, /V3 ASP 47, /V7 ARG 2, /V7 ASP 47, /V9 ARG
2, /V9 ASP 47, /W1 ARG 2, /W1 ASP 47, /W3 ARG 2, /W3 ASP 47, /W5 ARG 2, /W5
ASP 47, /W7 ARG 2, /W7 ASP 47, /W9 ARG 2, /W9 ASP 47, /X3 ARG 2, /X3 ASP 47,
/X5 ARG 2, /X5 ASP 47, /X7 ARG 2, /X7 ASP 47, /X9 ARG 2, /X9 ASP 47, /Y1 ARG
2, /Y1 ASP 47, /Y3 ARG 2, /Y3 ASP 47, /Y5 ARG 2, /Y5 ASP 47, /Y9 ARG 2, /Y9
ASP 47, /Z1 ARG 2, /Z1 ASP 47, /Z3 ARG 2, /Z3 ASP 47, /Z5 ARG 2, /Z5 ASP 47,
/Z7 ARG 2, /Z7 ASP 47, /Z9 ARG 2, /Z9 ASP 47, /0B ARG 2, /0B ASP 47, /0F ARG
2, /0F ASP 47, /0H ARG 2, /0H ASP 47, /0J ARG 2, /0J ASP 47, /0L ARG 2, /0L
ASP 47, /0N ARG 2, /0N ASP 47, /0P ARG 2, /0P ASP 47, /0R ARG 2, /0R ASP 47,
/0V ARG 2, /0V ASP 47, /0X ARG 2, /0X ASP 47, /0Z ARG 2, /0Z ASP 47, /1B ARG
2, /1B ASP 47, /1D ARG 2, /1D ASP 47, /1F ARG 2, /1F ASP 47, /1H ARG 2, /1H
ASP 47, /1L ARG 2, /1L ASP 47, /1N ARG 2, /1N ASP 47, /1P ARG 2, /1P ASP 47,
/1R ARG 2, /1R ASP 47, /1T ARG 2, /1T ASP 47, /1V ARG 2, /1V ASP 47, /1X ARG
2, /1X ASP 47, /1Z ARG 2, /1Z ASP 47, /2B ARG 2, /2B ASP 47, /2D ARG 2, /2D
ASP 47, /2F ARG 2, /2F ASP 47, /2H ARG 2, /2H ASP 47, /2J ARG 2, /2J ASP 47,
/2L ARG 2, /2L ASP 47, /2N ARG 2, /2N ASP 47, /2P ARG 2, /2P ASP 47, /2R ARG
2, /2R ASP 47, /2T ARG 2, /2T ASP 47, /2V ARG 2, /2V ASP 47, /2X ARG 2, /2Z
ARG 2, /2Z ASP 47, /3B ARG 2, /3D ARG 2, /3D ASP 47, /3F ARG 2, /3F ASP 47,
/3H ARG 2, /3H ASP 47, /3J ARG 2, /3J ASP 47, /3L ARG 2, /3L ASP 47, /3N ARG
2, /3N ASP 47, /3P ARG 2, /3P ASP 47, /3R ARG 2, /3T ARG 2, /3T ASP 47, /3V
LYS 101, /3X LYS 101, /3Z LYS 101, /4B LYS 101, /4D LYS 101, /4F LYS 101, /4H
LYS 101, /4J LYS 101, /4L ALA 242, /4M PRO 7, /4M PRO 98, /4N SER 446, /4O HIS
20, /4P HIS 20, /4Q ASP 305, /4R GLY 2, /4S GLY 2, /4T HIS 174, /4U GLY 2, /4V
GLU 391, /4W GLU 102, /4W GLN 323, /4X GLU 92, /4Y LEU 323, /4Z THR 20, /5A
GLN 255, /5B THR 76, /5C ASP 130, /5D ASP 130, /5F ARG 158, /5G LYS 249, /5H
SER 2, /5I SER 2, /5J SER 2, /5K SER 2, /5L ALA 2, /5M ALA 2, /5N ALA 2, /5O
ASN 4, /5P ASN 4, /5Q PHE 3, /5R PRO 45, /5S GLU 3, /5S ASN 101, /5S SER 174,
/5T GLU 3, /5T ASN 101, /5T SER 174, /5U GLU 3, /5U ASN 101, /5U SER 174, /5V
ASN 101, /5V SER 174, /5X VAL 5, /5Y VAL 5, /5Z VAL 5, /6A VAL 5, /6B VAL 5,
/6C VAL 5, /6D VAL 5, /6E THR 5, /6E SER 58, /6F ARG 2, /6F GLU 309, /6G LEU
11, /6G SER 36, /6G VAL 111, /6H LEU 11, /6H SER 36, /6I PRO 9, /6I VAL 305,
/6I ASP 342, /6J PRO 9, /6J VAL 305, /6J ASP 342, /6K PRO 9, /6K VAL 305, /6K
ASP 342, /6L PRO 9, /6L VAL 305, /6L ASP 342, /6M PRO 9, /6M VAL 305, /6M ASP
342, /6N PRO 9, /6N VAL 305, /6N ASP 342, /6O PRO 9, /6O VAL 305, /6O ASP 342,
/6P PRO 9, /6P ASN 101, /6P VAL 305, /6P ASP 342, /6T PRO 6, /6T ASP 80, /6T
ASP 241, /6T GLY 495, /6T GLY 590, /6T SER 625, /6U PRO 6, /6U ASP 80, /6U ASP
241, /6U GLY 590, /6U SER 625, /6V PRO 6, /6V THR 81, /6V ASP 241, /6V GLY
495, /6V GLY 590, /6V SER 625, /6W PRO 6, /6W ASP 80, /6W ASP 241, /6W GLY
495, /6W GLY 590, /6W SER 625, /6X PRO 6, /6X ASP 80, /6X ASP 241, /6X GLY
495, /6X GLY 590, /6X SER 625, /6Y PRO 6, /6Y LYS 84, /6Y ASP 241, /6Y GLY
495, /6Y GLY 590, /6Y SER 625, /6Z PRO 6, /6Z ASP 80, /6Z ASP 241, /6Z GLY
495, /6Z GLY 590, /6Z SER 625, /7A GLY 4, /7A ASP 80, /7C PRO 5, /7C THR 57,
/7D SER 15, /7E SER 15, /7F SER 15, /7G TYR 4, /7G GLY 63, /7H GLY 300, /7H
LEU 392, /7I VAL 2, /7I ASP 155, /7I THR 212, /7J ALA 80, /7J ASP 155, /7J THR
212, /7K SER 2, /7K ASN 93, /7K GLY 224, /7K GLY 433, /7L GLY 265, /7L GLY
433, /7M SER 2, /7N SER 2, /7O SER 12, /7O ILE 60, /7P VAL 15, /7P ILE 60, /7Q
SER 119, /7R GLU 84, /7S GLU 119, /7T LYS 30, /7T PRO 67, /7U PRO 67, /7V LYS
13, /7V TYR 89, /7W LYS 13, /7W TYR 89, /7X GLY 300, /7X LEU 392, /7Y ILE 8,
/8A VAL 156, /8B VAL 156, /8C VAL 156, /8D LEU 57, /8D VAL 156  
Chain-final residues that are actual C termini: /4Q ARG 367, /4R ARG 367, /4T
ARG 367, /6E GLU 268, /7D ASN 146, /7E ASN 146, /7F ASN 146, /7G PRO 235, /7Q
PHE 189  
Chain-final residues that are not actual C termini: /1 GLN 426, /2 ALA 437, /3
GLU 433, /4 ALA 437, /5 PHE 436, /6 ALA 437, /7 GLU 437, /8 ALA 437, /9 PHE
436, /A0 ALA 437, /A1 GLU 432, /A2 ALA 437, /A3 GLU 435, /A4 ALA 437, /A5 ALA
430, /A7 GLN 426, /A8 PRO 37, /A8 ALA 437, /A9 GLN 426, /B0 PRO 37, /B0 ALA
437, /B1 GLN 426, /B2 PRO 37, /B2 ALA 437, /B3 GLN 426, /B4 PRO 37, /B4 ALA
437, /B5 GLN 426, /B7 PRO 37, /B7 ALA 437, /B8 GLN 426, /B9 PRO 37, /B9 ALA
437, /C0 GLN 426, /C1 PRO 37, /C1 ALA 437, /C2 GLN 426, /C4 GLN 426, /C5 ALA
437, /C6 GLN 426, /C7 ALA 437, /C8 GLN 426, /C9 PRO 37, /C9 ALA 437, /D0 GLN
426, /D1 PRO 37, /D1 ALA 437, /D2 GLN 426, /D3 SER 38, /D3 ALA 437, /D4 GLN
426, /D5 PRO 37, /D5 ALA 437, /D6 GLN 426, /D7 SER 38, /D7 ALA 437, /D8 GLN
426, /E0 GLN 426, /E1 SER 38, /E1 ALA 437, /E2 GLN 426, /E3 PRO 37, /E3 ALA
437, /E4 GLN 426, /E5 PRO 37, /E5 ALA 437, /E6 GLN 426, /E7 SER 38, /E7 ALA
437, /E8 GLN 426, /E9 PRO 37, /E9 ALA 437, /F0 GLN 426, /F1 PRO 37, /F1 ALA
437, /F2 GLN 426, /F3 PRO 37, /F3 ALA 437, /F5 PRO 37, /F5 ALA 437, /F6 GLN
426, /F7 PRO 37, /F7 ALA 437, /F8 GLN 426, /F9 ALA 437, /G0 GLN 426, /G1 ALA
437, /G2 GLN 426, /G3 ALA 437, /G4 GLN 426, /G5 PRO 37, /G5 ALA 437, /G6 GLN
426, /G7 PRO 37, /G7 ALA 437, /G8 GLN 426, /G9 PRO 37, /G9 ALA 437, /H1 PRO
37, /H1 ALA 437, /H2 GLN 426, /H3 PRO 37, /H3 ALA 437, /H4 GLN 426, /H5 PRO
37, /H5 ALA 437, /H6 GLN 426, /H7 PRO 37, /H7 ALA 437, /H8 GLN 426, /H9 PRO
37, /H9 ALA 437, /I0 GLN 426, /I1 PRO 37, /I1 ALA 437, /I2 GLN 426, /I3 PRO
37, /I3 ALA 437, /I4 GLN 426, /I5 PRO 37, /I5 ALA 437, /I7 ASP 39, /I7 ALA
437, /I8 GLN 426, /I9 SER 38, /I9 ALA 437, /J0 GLN 426, /J1 PRO 37, /J1 ALA
437, /J2 GLN 426, /J3 PRO 37, /J3 ALA 437, /J4 GLN 426, /J5 GLU 438, /J6 GLN
426, /J7 PRO 37, /J7 ALA 437, /J8 GLN 426, /J9 GLU 438, /K0 GLN 426, /K1 PRO
37, /K1 ALA 437, /K3 PRO 37, /K3 ALA 437, /K4 GLN 426, /K5 PRO 37, /K5 ALA
437, /K6 GLN 426, /K7 PRO 37, /K7 ALA 437, /K8 GLN 426, /K9 PRO 37, /K9 ALA
437, /L0 GLN 426, /L1 PRO 37, /L1 ALA 437, /L2 GLN 426, /L3 PRO 37, /L3 ALA
437, /L4 GLN 426, /L5 PRO 37, /L5 ALA 437, /L6 GLN 426, /L7 PRO 37, /L7 ALA
437, /L9 PRO 37, /L9 ALA 437, /M0 GLN 426, /M1 PRO 37, /M1 ALA 437, /M2 GLN
426, /M3 ALA 437, /M4 GLN 426, /M5 PRO 37, /M5 ALA 437, /M6 GLN 426, /M7 ALA
437, /M8 GLN 426, /M9 GLU 438, /N0 GLN 426, /N1 SER 38, /N1 ALA 437, /N2 GLN
426, /N3 PRO 37, /N3 ALA 437, /N5 PRO 37, /N5 ALA 437, /N6 GLN 426, /N7 PRO
37, /N7 ALA 437, /N8 GLN 426, /N9 PRO 37, /N9 ALA 437, /O0 GLN 426, /O1 PRO
37, /O1 ALA 437, /O2 GLN 426, /O3 PRO 37, /O3 ALA 437, /O4 GLN 426, /O5 PRO
37, /O5 ALA 437, /O6 GLN 426, /O7 SER 38, /O7 ALA 437, /O8 GLN 426, /O9 PRO
37, /O9 ALA 437, /P3 PRO 37, /P3 ALA 437, /P4 GLN 426, /P5 ALA 437, /P6 GLN
426, /P7 PRO 37, /P7 ALA 437, /P8 GLN 426, /P9 ALA 437, /Q0 GLN 426, /Q1 PRO
37, /Q1 ALA 437, /Q2 GLN 426, /Q3 PRO 37, /Q3 ALA 437, /Q4 GLN 426, /Q5 PRO
37, /Q5 ALA 437, /Q6 GLN 426, /Q8 GLN 426, /Q9 PRO 37, /Q9 ALA 437, /R0 GLY
434, /R1 PRO 37, /R1 ALA 437, /R2 GLN 426, /R3 PRO 37, /R3 GLU 438, /R4 ALA
430, /R5 ALA 437, /R6 GLN 426, /R7 PRO 37, /R7 ALA 437, /R8 GLU 431, /R9 ALA
437, /S0 GLN 426, /S1 PRO 37, /S1 SER 439, /S2 GLU 431, /S4 ASP 427, /S5 PRO
37, /S5 ALA 437, /S6 GLN 426, /S7 ALA 437, /S8 GLN 426, /S9 PRO 37, /S9 ALA
437, /T0 GLN 426, /T1 PRO 37, /T1 ALA 437, /T2 GLN 426, /T3 PRO 37, /T3 ALA
437, /T4 GLN 426, /T5 PRO 37, /T5 ALA 437, /T6 GLN 426, /T7 PRO 37, /T7 ALA
437, /T8 GLN 426, /U1 PRO 37, /U1 ALA 437, /U2 GLN 426, /U3 PRO 37, /U3 ALA
437, /U4 GLN 426, /U5 PRO 37, /U5 ALA 437, /U6 GLN 426, /U7 PRO 37, /U7 ALA
437, /U8 ALA 430, /U9 PRO 37, /U9 ALA 437, /V0 GLN 426, /V1 PRO 37, /V1 ALA
437, /V2 GLN 426, /V3 PRO 37, /V3 ALA 437, /V4 GLN 426, /V6 GLN 426, /V7 PRO
37, /V7 ALA 437, /V8 GLN 426, /V9 PRO 37, /V9 ALA 437, /W0 GLN 426, /W1 PRO
37, /W1 ALA 437, /W2 GLN 426, /W3 PRO 37, /W3 ALA 437, /W4 GLN 426, /W5 PRO
37, /W5 ALA 437, /W6 GLN 426, /W7 PRO 37, /W7 ALA 437, /W8 GLN 426, /W9 PRO
37, /W9 ALA 437, /X0 GLN 426, /X2 GLN 426, /X3 PRO 37, /X3 ALA 437, /X4 GLN
426, /X5 PRO 37, /X5 ALA 437, /X6 GLN 426, /X7 PRO 37, /X7 ALA 437, /X8 GLN
426, /X9 PRO 37, /X9 ALA 437, /Y0 GLN 426, /Y1 PRO 37, /Y1 ALA 437, /Y2 GLN
426, /Y3 PRO 37, /Y3 ALA 437, /Y4 GLN 426, /Y5 PRO 37, /Y5 ALA 437, /Y6 GLN
426, /Y8 GLN 426, /Y9 PRO 37, /Y9 ALA 437, /Z0 GLN 426, /Z1 PRO 37, /Z1 ALA
437, /Z2 GLN 426, /Z3 PRO 37, /Z3 ALA 437, /Z4 GLN 426, /Z5 PRO 37, /Z5 ALA
437, /Z6 GLN 426, /Z7 PRO 37, /Z7 ALA 437, /Z8 GLN 426, /Z9 PRO 37, /Z9 ALA
437, /0A GLN 426, /0B PRO 37, /0B ALA 437, /0C GLN 426, /0E GLN 426, /0F PRO
37, /0F ALA 437, /0G GLN 426, /0H PRO 37, /0H ALA 437, /0I GLN 426, /0J PRO
37, /0J ALA 437, /0K GLN 426, /0L PRO 37, /0L ALA 437, /0M GLN 426, /0N PRO
37, /0N ALA 437, /0O GLN 426, /0P PRO 37, /0P ALA 437, /0Q GLN 426, /0R PRO
37, /0R ALA 437, /0S GLN 426, /0U GLN 426, /0V PRO 37, /0V ALA 437, /0W GLN
426, /0X PRO 37, /0X ALA 437, /0Y GLN 426, /0Z PRO 37, /0Z ALA 437, /1A GLN
426, /1B PRO 37, /1B ALA 437, /1C GLN 426, /1D PRO 37, /1D ALA 437, /1E GLN
426, /1F PRO 37, /1F ALA 437, /1G GLN 426, /1H PRO 37, /1H ALA 437, /1K GLN
426, /1L PRO 37, /1L ALA 437, /1M GLN 426, /1N PRO 37, /1N ALA 437, /1O GLN
426, /1P PRO 37, /1P ALA 437, /1Q GLN 426, /1R PRO 37, /1R ALA 437, /1S GLN
426, /1T PRO 37, /1T ALA 437, /1U GLN 426, /1V PRO 37, /1V ALA 437, /1W GLN
426, /1X PRO 37, /1X ALA 437, /1Z PRO 37, /1Z ALA 437, /2A GLN 426, /2B PRO
37, /2B ALA 437, /2C GLN 426, /2D PRO 37, /2D ALA 437, /2E GLN 426, /2F PRO
37, /2F ALA 437, /2G GLN 426, /2H PRO 37, /2H ALA 437, /2I GLN 426, /2J PRO
37, /2J ALA 437, /2K GLN 426, /2L PRO 37, /2L ALA 437, /2M GLN 426, /2N PRO
37, /2N ALA 437, /2P PRO 37, /2P ALA 437, /2Q GLN 426, /2R PRO 37, /2R ALA
437, /2S GLN 426, /2T PRO 37, /2T ALA 437, /2U GLN 426, /2V PRO 37, /2V ALA
437, /2W GLN 426, /2X GLU 438, /2Y GLN 426, /2Z PRO 37, /2Z ALA 437, /3A GLN
426, /3B GLU 438, /3C GLN 426, /3D PRO 37, /3D ALA 437, /3F PRO 37, /3F ALA
437, /3G GLN 426, /3H PRO 37, /3H ALA 437, /3I GLN 426, /3J PRO 37, /3J ALA
437, /3K GLN 426, /3L PRO 37, /3L ALA 437, /3M GLN 426, /3N PRO 37, /3N ALA
437, /3O GLN 426, /3P PRO 37, /3P ALA 437, /3Q GLN 426, /3R GLU 438, /3S GLN
426, /3T PRO 37, /3T ALA 437, /3V LYS 93, /3V VAL 304, /3W PHE 184, /3X LYS
93, /3X VAL 304, /3Y PHE 184, /3Z LYS 93, /3Z VAL 304, /4A PHE 184, /4B LYS
93, /4B VAL 304, /4C PHE 184, /4D LYS 93, /4D VAL 304, /4E PHE 184, /4F LYS
93, /4F VAL 304, /4G PHE 184, /4H LYS 93, /4H VAL 304, /4I PHE 184, /4J VAL
304, /4L LYS 479, /4M SER 94, /4M MET 325, /4N ASN 497, /4O ASN 497, /4P ALA
213, /4S GLN 46, /4U GLU 284, /4V LYS 473, /4W ARG 303, /4W LYS 473, /4X THR
150, /4Y LYS 448, /4Z ALA 408, /5A GLU 482, /5B GLU 324, /5C ILE 499, /5D ARG
235, /5E SER 258, /5F ALA 149, /5F LEU 389, /5G LEU 389, /5H PHE 136, /5I PHE
136, /5J PHE 136, /5K PHE 136, /5L PRO 627, /5M PRO 627, /5N PRO 627, /5O ALA
379, /5P ALA 379, /5Q GLY 193, /5R LYS 66, /5S GLU 92, /5S LYS 149, /5S GLU
233, /5T GLU 92, /5T LYS 149, /5T GLY 232, /5U GLU 92, /5U LYS 149, /5U GLU
233, /5V LYS 149, /5V GLU 233, /5X GLU 225, /5Y GLU 225, /5Z GLU 225, /6A GLU
225, /6B GLU 225, /6C GLU 225, /6D GLU 225, /6E ASP 48, /6F PRO 303, /6F ALA
400, /6G ARG 28, /6G PRO 101, /6G GLN 209, /6H ALA 29, /6H GLN 209, /6I PHE
297, /6I THR 334, /6I ASN 351, /6J PHE 297, /6J THR 334, /6J ASN 351, /6K PHE
297, /6K THR 334, /6K ASN 351, /6L PHE 297, /6L THR 334, /6L ASN 351, /6M PHE
297, /6M THR 334, /6M ASN 351, /6N PHE 297, /6N THR 334, /6N ASN 351, /6O PHE
297, /6O THR 334, /6O ASN 351, /6P CYS 68, /6P PHE 297, /6P THR 334, /6P ASN
351, /6Q PHE 85, /6R PHE 85, /6S PHE 85, /6T ALA 46, /6T ARG 223, /6T GLY 491,
/6T ALA 580, /6T THR 621, /6T GLY 634, /6U VAL 48, /6U ARG 223, /6U ALA 580,
/6U THR 621, /6U GLY 634, /6V ALA 44, /6V ARG 223, /6V GLY 491, /6V ALA 580,
/6V THR 621, /6V GLY 634, /6W VAL 48, /6W ARG 223, /6W GLY 491, /6W ALA 580,
/6W THR 621, /6W GLY 634, /6X LEU 51, /6X ARG 223, /6X GLY 491, /6X ALA 580,
/6X THR 621, /6X GLY 634, /6Y VAL 48, /6Y ARG 223, /6Y GLY 491, /6Y ALA 580,
/6Y THR 621, /6Y GLY 634, /6Z LEU 45, /6Z ARG 223, /6Z GLY 491, /6Z ALA 580,
/6Z THR 621, /6Z GLY 634, /7A VAL 48, /7A ARG 223, /7B GLY 97, /7C SER 48, /7C
ARG 110, /7G HIS 54, /7H GLY 364, /7H VAL 464, /7I SER 151, /7I LEU 173, /7I
MET 270, /7J SER 151, /7J LEU 173, /7J MET 482, /7K LYS 85, /7K VAL 216, /7K
GLY 417, /7K GLN 453, /7L GLY 417, /7L GLU 455, /7M ALA 86, /7N LYS 127, /7O
LYS 39, /7O GLN 90, /7P LYS 39, /7P LYS 216, /7R ARG 278, /7S ARG 278, /7T SER
61, /7T GLN 247, /7U GLN 247, /7V ASP 85, /7V ASP 104, /7W ASP 85, /7W ASP
104, /7X GLY 364, /7X VAL 464, /7Y PRO 254, /7Z LYS 39, /8A LYS 129, /8A PRO
233, /8B LYS 129, /8B ASP 239, /8C LYS 129, /8C ASP 239, /8D LYS 129, /8D ASP
239  
Missing OXT added to C-terminal residue /4Q ARG 367  
Missing OXT added to C-terminal residue /4R ARG 367  
Missing OXT added to C-terminal residue /4T ARG 367  
Missing OXT added to C-terminal residue /6E GLU 268  
Missing OXT added to C-terminal residue /7D ASN 146  
4 messages similar to the above omitted  
139801 hydrogen bonds  
Adding 'H' to /1 LEU 289  
Adding 'H' to /2 ARG 2  
Adding 'H' to /4 ARG 2  
Adding 'H' to /6 ARG 2  
Adding 'H' to /8 ARG 2  
473 messages similar to the above omitted  
/1 GLN 426 is not terminus, removing H atom from 'C'  
/2 ALA 437 is not terminus, removing H atom from 'C'  
/3 GLU 433 is not terminus, removing H atom from 'C'  
/4 ALA 437 is not terminus, removing H atom from 'C'  
/5 PHE 436 is not terminus, removing H atom from 'C'  
677 messages similar to the above omitted  
1322626 hydrogens added  
  

> toolshed show Shell




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:11df]
	Kernel driver in use: nvidia

[Eric Pettersen]

Well, obviously a chain is a series of connected polymeric residues, which is not what this modeler is doing. In such a case, you get what you get. These bound valines should have been treated in the input file the same way as any other bound ligand, which in PDB terms would mean: same chain ID as the chain it's bound to, but placed and numbered after the TER card record for that chain, with appropriate CONECT/LINK records.