Opened 4 years ago

Closed 4 years ago

#4780 closed defect (limitation)

ISOLDE: possible error in MD template

Reported by: caillancm@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.4 (2021-05-14 07:23:00 UTC)
Description
Using ISOLDE,  after paramaterising a putrescine residue with the built-in MC_PUT template,  addh fails.  The error message (which doesn't seem to be included in the log) is:

Failed to add atoms ['H23'] to atom N1 because this will lead to having 5 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (MC_PUT). If this template is built into ISOLDE, please report this using Help/Report a bug

Log:
UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/crowe/Desktop/phenix/poxtA/ReadySet_88/210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb

Chain information for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
A | No description available  
B | No description available  
D | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> set bgColor white

> open /Users/crowe/Dropbox/poxtA/50-59_maps/58_rescaled-
> maps/mb/combined/chimeraX-volMax-pp.mrc

Opened chimeraX-volMax-pp.mrc as #2, grid size 360,360,360, pixel 0.82, shown
at level 0.0392, step 2, values float32  

> open /Users/crowe/Dropbox/poxtA/50-59_maps/58_rescaled-
> maps/mb/combined/chimeraX-volMax.mrc

Opened chimeraX-volMax.mrc as #3, grid size 360,360,360, pixel 0.82, shown at
level 0.0239, step 2, values float32  

> clipper associate #2 toModel #1

Opened chimeraX-volMax-pp.mrc as #1.1.1.1, grid size 360,360,360, pixel 0.82,
shown at level 0.0296, step 1, values float32  
Chain information for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb  
---  
Chain | Description  
1.2/0 | No description available  
1.2/1 | No description available  
1.2/2 | No description available  
1.2/3 | No description available  
1.2/4 | No description available  
1.2/5 | No description available  
1.2/6 | No description available  
1.2/7 | No description available  
1.2/8 | No description available  
1.2/A | No description available  
1.2/B | No description available  
1.2/D | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
1.2/J | No description available  
1.2/K | No description available  
1.2/M | No description available  
1.2/N | No description available  
1.2/O | No description available  
1.2/P | No description available  
1.2/Q | No description available  
1.2/R | No description available  
1.2/S | No description available  
1.2/T | No description available  
1.2/U | No description available  
1.2/V | No description available  
1.2/W | No description available  
1.2/X | No description available  
1.2/Y | No description available  
1.2/Z | No description available  
1.2/a | No description available  
1.2/b | No description available  
1.2/c | No description available  
1.2/d | No description available  
1.2/e | No description available  
1.2/f | No description available  
1.2/g | No description available  
1.2/h | No description available  
1.2/i | No description available  
1.2/j | No description available  
1.2/k | No description available  
1.2/l | No description available  
1.2/m | No description available  
1.2/n | No description available  
1.2/o | No description available  
1.2/p | No description available  
1.2/q | No description available  
1.2/r | No description available  
1.2/s | No description available  
1.2/t | No description available  
1.2/u | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  
Loading residue template for ATP from internal database  
Loading residue template for PUT from internal database  
Loading residue template for SCM from internal database  
Deleted the following atoms from residue A b3: OP1  
Deleted the following atoms from residue A a1561: OP1  
Deleted the following atoms from residue A a1540: OP1  
Deleted the following atoms from residue A a1534: OP1  
Deleted the following atoms from residue A a1526: OP1  
Deleted the following atoms from residue A a1510: OP1  
Deleted the following atoms from residue A a1507: OP1  
Deleted the following atoms from residue A a1505: OP1  
Deleted the following atoms from residue A a1503: OP1  
Deleted the following atoms from residue A a1496: OP1  
Deleted the following atoms from residue A a1495: OP1  
Deleted the following atoms from residue A a1487: OP1  
Deleted the following atoms from residue A a1454: OP1  
Deleted the following atoms from residue A a1452: OP1  
Deleted the following atoms from residue A a1442: OP1  
Deleted the following atoms from residue A a1439: OP1  
Deleted the following atoms from residue A a1436: OP1  
Deleted the following atoms from residue A a1424: OP1  
Deleted the following atoms from residue A a1422: OP1  
Deleted the following atoms from residue A a1401: OP1  
Deleted the following atoms from residue A a1389: OP1  
Deleted the following atoms from residue A a1386: OP1  
Deleted the following atoms from residue A a1383: OP1  
Deleted the following atoms from residue A a1376: OP1  
Deleted the following atoms from residue A a1375: OP1  
Deleted the following atoms from residue A a1372: OP1  
Deleted the following atoms from residue A a1366: OP1  
Deleted the following atoms from residue A a1365: OP1  
Deleted the following atoms from residue A a1358: OP1  
Deleted the following atoms from residue A a1355: OP1  
Deleted the following atoms from residue A a1345: OP1  
Deleted the following atoms from residue A a1337: OP1  
Deleted the following atoms from residue A a1332: OP1  
Deleted the following atoms from residue A a1315: OP1  
Deleted the following atoms from residue A a1314: OP1  
Deleted the following atoms from residue A a1306: OP1  
Deleted the following atoms from residue A a1300: OP1  
Deleted the following atoms from residue A a1289: OP1  
Deleted the following atoms from residue A a1287: OP1  
Deleted the following atoms from residue A a1280: OP1  
Deleted the following atoms from residue A a1276: OP1  
Deleted the following atoms from residue A a1274: OP1  
Deleted the following atoms from residue A a1271: OP1  
Deleted the following atoms from residue A a1270: OP1  
Deleted the following atoms from residue A a1265: OP1  
Deleted the following atoms from residue A a1264: OP1  
Deleted the following atoms from residue A a1262: OP1  
Deleted the following atoms from residue A a1255: OP1  
Deleted the following atoms from residue A a1253: OP1  
Deleted the following atoms from residue A a1251: OP1  
Deleted the following atoms from residue A a1242: OP1  
Deleted the following atoms from residue A a1239: OP1  
Deleted the following atoms from residue A a1230: OP1  
Deleted the following atoms from residue A a1227: OP1  
Deleted the following atoms from residue A a1224: OP1  
Deleted the following atoms from residue A a1223: OP1  
Deleted the following atoms from residue A a1217: OP1  
Deleted the following atoms from residue A a1202: OP1  
Deleted the following atoms from residue A a1197: OP1  
Deleted the following atoms from residue A a1196: OP1  
Deleted the following atoms from residue A a1183: OP1  
Deleted the following atoms from residue A a1181: OP1  
Deleted the following atoms from residue A a1177: OP1  
Deleted the following atoms from residue A a1172: OP1  
Deleted the following atoms from residue A a1164: OP1  
Deleted the following atoms from residue A a1160: OP1  
Deleted the following atoms from residue A a1157: OP1  
Deleted the following atoms from residue A a1150: OP1  
Deleted the following atoms from residue A a1144: OP1  
Deleted the following atoms from residue A a1137: OP1  
Deleted the following atoms from residue A a1132: OP1  
Deleted the following atoms from residue A a1129: OP1  
Deleted the following atoms from residue A a1109: OP1  
Deleted the following atoms from residue A a1094: OP1  
Deleted the following atoms from residue A a1082: OP1  
Deleted the following atoms from residue A a1071: OP1  
Deleted the following atoms from residue A a1067: OP1  
Deleted the following atoms from residue A a1066: OP1  
Deleted the following atoms from residue A a1047: OP1  
Deleted the following atoms from residue A a1045: OP1  
Deleted the following atoms from residue A a1041: OP1  
Deleted the following atoms from residue A a1039: OP1  
Deleted the following atoms from residue A a1034: OP1  
Deleted the following atoms from residue A a1023: OP1  
Deleted the following atoms from residue A a1013: OP1  
Deleted the following atoms from residue A a1010: OP1  
Deleted the following atoms from residue A a1005: OP1  
Deleted the following atoms from residue A a1004: OP1  
Deleted the following atoms from residue A a992: OP1  
Deleted the following atoms from residue A a991: OP1  
Deleted the following atoms from residue A a986: OP1  
Deleted the following atoms from residue A a976: OP1  
Deleted the following atoms from residue A a973: OP1  
Deleted the following atoms from residue A a964: OP1  
Deleted the following atoms from residue A a962: OP1  
Deleted the following atoms from residue A a950: OP1  
Deleted the following atoms from residue A a945: OP1  
Deleted the following atoms from residue A a942: OP1  
Deleted the following atoms from residue A a936: OP1  
Deleted the following atoms from residue A a934: OP1  
Deleted the following atoms from residue A a928: OP1  
Deleted the following atoms from residue A a922: OP1  
Deleted the following atoms from residue A a916: OP1  
Deleted the following atoms from residue A a903: OP1  
Deleted the following atoms from residue A a900: OP1  
Deleted the following atoms from residue A a899: OP1  
Deleted the following atoms from residue A a896: OP1  
Deleted the following atoms from residue A a892: OP1  
Deleted the following atoms from residue A a890: OP1  
Deleted the following atoms from residue A a887: OP1  
Deleted the following atoms from residue A a879: OP1  
Deleted the following atoms from residue A a863: OP1  
Deleted the following atoms from residue A a855: OP1  
Deleted the following atoms from residue A a854: OP1  
Deleted the following atoms from residue A a848: OP1  
Deleted the following atoms from residue A a842: OP1  
Deleted the following atoms from residue A a841: OP1  
Deleted the following atoms from residue A a840: OP1  
Deleted the following atoms from residue A a833: OP1  
Deleted the following atoms from residue A a828: OP1  
Deleted the following atoms from residue A a818: OP1  
Deleted the following atoms from residue A a810: OP1  
Deleted the following atoms from residue A a807: OP1  
Deleted the following atoms from residue A a806: OP1  
Deleted the following atoms from residue A a803: OP1  
Deleted the following atoms from residue A a794: OP1  
Deleted the following atoms from residue A a785: OP1  
Deleted the following atoms from residue A a775: OP1  
Deleted the following atoms from residue A a742: OP1  
Deleted the following atoms from residue A a738: OP1  
Deleted the following atoms from residue A a734: OP1  
Deleted the following atoms from residue A a732: OP1  
Deleted the following atoms from residue A a730: OP1  
Deleted the following atoms from residue A a707: OP1  
Deleted the following atoms from residue A a702: OP1  
Deleted the following atoms from residue A a696: OP1  
Deleted the following atoms from residue A a694: OP1  
Deleted the following atoms from residue A a691: OP1  
Deleted the following atoms from residue A a689: OP1  
Deleted the following atoms from residue A a688: OP1  
Deleted the following atoms from residue A a686: OP1  
Deleted the following atoms from residue A a681: OP1  
Deleted the following atoms from residue A a674: OP1  
Deleted the following atoms from residue A a668: OP1  
Deleted the following atoms from residue A a667: OP1  
Deleted the following atoms from residue A a666: OP1  
Deleted the following atoms from residue A a648: OP1  
Deleted the following atoms from residue A a635: OP1  
Deleted the following atoms from residue A a634: OP1  
Deleted the following atoms from residue A a633: OP1  
Deleted the following atoms from residue A a628: OP1  
Deleted the following atoms from residue A a622: OP1  
Deleted the following atoms from residue A a621: OP1  
Deleted the following atoms from residue A a609: OP1  
Deleted the following atoms from residue A a604: OP1  
Deleted the following atoms from residue A a598: OP1  
Deleted the following atoms from residue A a589: OP1  
Deleted the following atoms from residue A a565: OP1  
Deleted the following atoms from residue A a559: OP1  
Deleted the following atoms from residue A a539: OP1  
Deleted the following atoms from residue A a529: OP1  
Deleted the following atoms from residue A a525: OP1  
Deleted the following atoms from residue A a523: OP1  
Deleted the following atoms from residue A a521: OP1  
Deleted the following atoms from residue A a517: OP1  
Deleted the following atoms from residue A a508: OP1  
Deleted the following atoms from residue A a498: OP1  
Deleted the following atoms from residue A a497: OP1  
Deleted the following atoms from residue A a492: OP1  
Deleted the following atoms from residue A a489: OP1  
Deleted the following atoms from residue A a484: OP1  
Deleted the following atoms from residue A a480: OP1  
Deleted the following atoms from residue A a478: OP1  
Deleted the following atoms from residue A a477: OP1  
Deleted the following atoms from residue A a472: OP1  
Deleted the following atoms from residue A a470: OP1  
Deleted the following atoms from residue A a459: OP1  
Deleted the following atoms from residue A a458: OP1  
Deleted the following atoms from residue A a457: OP1  
Deleted the following atoms from residue A a456: OP1  
Deleted the following atoms from residue A a451: OP1  
Deleted the following atoms from residue A a440: OP1  
Deleted the following atoms from residue A a433: OP1  
Deleted the following atoms from residue A a423: OP1  
Deleted the following atoms from residue A a422: OP1  
Deleted the following atoms from residue A a419: OP1  
Deleted the following atoms from residue A a415: OP1  
Deleted the following atoms from residue A a408: OP1  
Deleted the following atoms from residue A a404: OP1  
Deleted the following atoms from residue A a400: OP1  
Deleted the following atoms from residue A a399: OP1  
Deleted the following atoms from residue A a385: OP1  
Deleted the following atoms from residue A a382: OP1  
Deleted the following atoms from residue A a379: OP1  
Deleted the following atoms from residue A a375: OP1  
Deleted the following atoms from residue A a364: OP1  
Deleted the following atoms from residue A a362: OP1  
Deleted the following atoms from residue A a355: OP1  
Deleted the following atoms from residue A a353: OP1  
Deleted the following atoms from residue A a347: OP1  
Deleted the following atoms from residue A a341: OP1  
Deleted the following atoms from residue A a339: OP1  
Deleted the following atoms from residue A a319: OP1  
Deleted the following atoms from residue A a312: OP1  
Deleted the following atoms from residue A a308: OP1  
Deleted the following atoms from residue A a300: OP1  
Deleted the following atoms from residue A a299: OP1  
Deleted the following atoms from residue A a296: OP1  
Deleted the following atoms from residue A a284: OP1  
Deleted the following atoms from residue A a272: OP1  
Deleted the following atoms from residue A a269: OP1  
Deleted the following atoms from residue A a258: OP1  
Deleted the following atoms from residue A a250: OP1  
Deleted the following atoms from residue A a228: OP1  
Deleted the following atoms from residue A a227: OP1  
Deleted the following atoms from residue A a223: OP1  
Deleted the following atoms from residue A a221: OP1  
Deleted the following atoms from residue A a220: OP1  
Deleted the following atoms from residue A a218: OP1  
Deleted the following atoms from residue A a206: OP1  
Deleted the following atoms from residue A a196: OP1  
Deleted the following atoms from residue A a189: OP1  
Deleted the following atoms from residue A a188: OP1  
Deleted the following atoms from residue A a181: OP1  
Deleted the following atoms from residue A a169: OP1  
Deleted the following atoms from residue A a168: OP1  
Deleted the following atoms from residue A a166: OP1  
Deleted the following atoms from residue A a158: OP1  
Deleted the following atoms from residue A a155: OP1  
Deleted the following atoms from residue A a138: OP1  
Deleted the following atoms from residue A a136: OP1  
Deleted the following atoms from residue A a135: OP1  
Deleted the following atoms from residue A a132: OP1  
Deleted the following atoms from residue A a125: OP1  
Deleted the following atoms from residue A a117: OP1  
Deleted the following atoms from residue A a114: OP1  
Deleted the following atoms from residue A a68: OP1  
Deleted the following atoms from residue A a62: OP1  
Deleted the following atoms from residue A a57: OP1  
Deleted the following atoms from residue A a55: OP1  
Deleted the following atoms from residue A a35: OP1  
Deleted the following atoms from residue A a34: OP1  
Deleted the following atoms from residue A a31: OP1  
Deleted the following atoms from residue A a28: OP1  
Deleted the following atoms from residue A a18: OP1  
Deleted the following atoms from residue A a12: OP1  
Deleted the following atoms from residue A D59: OP1  
Deleted the following atoms from residue A D52: OP1  
Deleted the following atoms from residue A D44: OP1  
Deleted the following atoms from residue A D39: OP1  
Deleted the following atoms from residue A D36: OP1  
Deleted the following atoms from residue A D11: OP1  
Deleted the following atoms from residue A B113: OP1  
Deleted the following atoms from residue A B97: OP1  
Deleted the following atoms from residue A B81: OP1  
Deleted the following atoms from residue A B80: OP1  
Deleted the following atoms from residue A B76: OP1  
Deleted the following atoms from residue A B71: OP1  
Deleted the following atoms from residue A B64: OP1  
Deleted the following atoms from residue A B56: OP1  
Deleted the following atoms from residue A B51: OP1  
Deleted the following atoms from residue A B48: OP1  
Deleted the following atoms from residue A B46: OP1  
Deleted the following atoms from residue A B44: OP1  
Deleted the following atoms from residue A B27: OP1  
Deleted the following atoms from residue A B25: OP1  
Deleted the following atoms from residue A B20: OP1  
Deleted the following atoms from residue A B19: OP1  
Deleted the following atoms from residue A B17: OP1  
Deleted the following atoms from residue A A2909: OP1  
Deleted the following atoms from residue A A2904: OP1  
Deleted the following atoms from residue A A2901: OP1  
Deleted the following atoms from residue A A2893: OP1  
Deleted the following atoms from residue A A2892: OP1  
Deleted the following atoms from residue A A2887: OP1  
Deleted the following atoms from residue A A2886: OP1  
Deleted the following atoms from residue A A2878: OP1  
Deleted the following atoms from residue A A2872: OP1  
Deleted the following atoms from residue A A2866: OP1  
Deleted the following atoms from residue A A2861: OP1  
Deleted the following atoms from residue A A2855: OP1  
Deleted the following atoms from residue A A2847: OP1  
Deleted the following atoms from residue A A2845: OP1  
Deleted the following atoms from residue A A2839: OP1  
Deleted the following atoms from residue A A2836: OP1  
Deleted the following atoms from residue A A2833: OP1  
Deleted the following atoms from residue A A2829: OP1  
Deleted the following atoms from residue A A2822: OP1  
Deleted the following atoms from residue A A2820: OP1  
Deleted the following atoms from residue A A2816: OP1  
Deleted the following atoms from residue A A2815: OP1  
Deleted the following atoms from residue A A2814: OP1  
Deleted the following atoms from residue A A2796: OP1  
Deleted the following atoms from residue A A2794: OP1  
Deleted the following atoms from residue A A2789: OP1  
Deleted the following atoms from residue A A2778: OP1  
Deleted the following atoms from residue A A2777: OP1  
Deleted the following atoms from residue A A2771: OP1  
Deleted the following atoms from residue A A2770: OP1  
Deleted the following atoms from residue A A2766: OP1  
Deleted the following atoms from residue A A2762: OP1  
Deleted the following atoms from residue A A2761: OP1  
Deleted the following atoms from residue A A2755: OP1  
Deleted the following atoms from residue A A2754: OP1  
Deleted the following atoms from residue A A2753: OP1  
Deleted the following atoms from residue A A2751: OP1  
Deleted the following atoms from residue A A2742: OP1  
Deleted the following atoms from residue A A2738: OP1  
Deleted the following atoms from residue A A2734: OP1  
Deleted the following atoms from residue A A2724: OP1  
Deleted the following atoms from residue A A2719: OP1  
Deleted the following atoms from residue A A2706: OP1  
Deleted the following atoms from residue A A2703: OP1  
Deleted the following atoms from residue A A2692: OP1  
Deleted the following atoms from residue A A2688: OP1  
Deleted the following atoms from residue A A2684: OP1  
Deleted the following atoms from residue A A2678: OP1  
Deleted the following atoms from residue A A2670: OP1  
Deleted the following atoms from residue A A2654: OP1  
Deleted the following atoms from residue A A2647: OP1  
Deleted the following atoms from residue A A2646: OP1  
Deleted the following atoms from residue A A2645: OP1  
Deleted the following atoms from residue A A2627: OP1  
Deleted the following atoms from residue A A2615: OP1  
Deleted the following atoms from residue A A2613: OP1  
Deleted the following atoms from residue A A2611: OP1  
Deleted the following atoms from residue A A2603: OP1  
Deleted the following atoms from residue A A2590: OP1  
Deleted the following atoms from residue A A2585: OP1  
Deleted the following atoms from residue A A2579: OP1  
Deleted the following atoms from residue A A2574: OP1  
Deleted the following atoms from residue A A2555: OP1  
Deleted the following atoms from residue A A2554: OP1  
Deleted the following atoms from residue A A2531: OP1  
Deleted the following atoms from residue A A2516: OP1  
Deleted the following atoms from residue A A2510: OP1  
Deleted the following atoms from residue A A2501: OP1  
Deleted the following atoms from residue A A2495: OP1  
Deleted the following atoms from residue A A2491: OP1  
Deleted the following atoms from residue A A2484: OP1  
Deleted the following atoms from residue A A2482: OP1  
Deleted the following atoms from residue A A2472: OP1  
Deleted the following atoms from residue A A2463: OP1  
Deleted the following atoms from residue A A2447: OP1  
Deleted the following atoms from residue A A2446: OP1  
Deleted the following atoms from residue A A2445: OP1  
Deleted the following atoms from residue A A2443: OP1  
Deleted the following atoms from residue A A2438: OP1  
Deleted the following atoms from residue A A2431: OP1  
Deleted the following atoms from residue A A2424: OP1  
Deleted the following atoms from residue A A2420: OP1  
Deleted the following atoms from residue A A2405: OP1  
Deleted the following atoms from residue A A2391: OP1  
Deleted the following atoms from residue A A2390: OP1  
Deleted the following atoms from residue A A2386: OP1  
Deleted the following atoms from residue A A2382: OP1  
Deleted the following atoms from residue A A2374: OP1  
Deleted the following atoms from residue A A2371: OP1  
Deleted the following atoms from residue A A2367: OP1  
Deleted the following atoms from residue A A2359: OP1  
Deleted the following atoms from residue A A2353: OP1  
Deleted the following atoms from residue A A2346: OP1  
Deleted the following atoms from residue A A2342: OP1  
Deleted the following atoms from residue A A2341: OP1  
Deleted the following atoms from residue A A2327: OP1  
Deleted the following atoms from residue A A2324: OP1  
Deleted the following atoms from residue A A2314: OP1  
Deleted the following atoms from residue A A2313: OP1  
Deleted the following atoms from residue A A2311: OP1  
Deleted the following atoms from residue A A2291: OP1  
Deleted the following atoms from residue A A2286: OP1  
Deleted the following atoms from residue A A2281: OP1  
Deleted the following atoms from residue A A2280: OP1  
Deleted the following atoms from residue A A2279: OP1  
Deleted the following atoms from residue A A2260: OP1  
Deleted the following atoms from residue A A2254: OP1  
Deleted the following atoms from residue A A2248: OP1  
Deleted the following atoms from residue A A2246: OP1  
Deleted the following atoms from residue A A2240: OP1  
Deleted the following atoms from residue A A2238: OP1  
Deleted the following atoms from residue A A2225: OP1  
Deleted the following atoms from residue A A2221: OP1  
Deleted the following atoms from residue A A2218: OP1  
Deleted the following atoms from residue A A2211: OP1  
Deleted the following atoms from residue A A2203: OP1  
Deleted the following atoms from residue A A2200: OP1  
Deleted the following atoms from residue A A2189: OP1  
Deleted the following atoms from residue A A2186: OP1  
Deleted the following atoms from residue A A2171: OP1  
Deleted the following atoms from residue A A2160: OP1  
Deleted the following atoms from residue A A2155: OP1  
Deleted the following atoms from residue A A2154: OP1  
Deleted the following atoms from residue A A2149: OP1  
Deleted the following atoms from residue A A2147: OP1  
Deleted the following atoms from residue A A2144: OP1  
Deleted the following atoms from residue A A2136: OP1  
Deleted the following atoms from residue A A2132: OP1  
Deleted the following atoms from residue A A2127: OP1  
Deleted the following atoms from residue A A2121: OP1  
Deleted the following atoms from residue A A2119: OP1  
Deleted the following atoms from residue A A2116: OP1  
Deleted the following atoms from residue A A2107: OP1  
Deleted the following atoms from residue A A2103: OP1  
Deleted the following atoms from residue A A2101: OP1  
Deleted the following atoms from residue A A2095: OP1  
Deleted the following atoms from residue A A2090: OP1  
Deleted the following atoms from residue A A2084: OP1  
Deleted the following atoms from residue A A2080: OP1  
Deleted the following atoms from residue A A2073: OP1  
Deleted the following atoms from residue A A2067: OP1  
Deleted the following atoms from residue A A2064: OP1  
Deleted the following atoms from residue A A2062: OP1  
Deleted the following atoms from residue A A2050: OP1  
Deleted the following atoms from residue A A2046: OP1  
Deleted the following atoms from residue A A2043: OP1  
Deleted the following atoms from residue A A2036: OP1  
Deleted the following atoms from residue A A2033: OP1  
Deleted the following atoms from residue A A2027: OP1  
Deleted the following atoms from residue A A2026: OP1  
Deleted the following atoms from residue A A2018: OP1  
Deleted the following atoms from residue A A2016: OP1  
Deleted the following atoms from residue A A2014: OP1  
Deleted the following atoms from residue A A2011: OP1  
Deleted the following atoms from residue A A2010: OP1  
Deleted the following atoms from residue A A1994: OP1  
Deleted the following atoms from residue A A1982: OP1  
Deleted the following atoms from residue A A1979: OP1  
Deleted the following atoms from residue A A1973: OP1  
Deleted the following atoms from residue A A1966: OP1  
Deleted the following atoms from residue A A1950: OP1  
Deleted the following atoms from residue A A1949: OP1  
Deleted the following atoms from residue A A1945: OP1  
Deleted the following atoms from residue A A1932: OP1  
Deleted the following atoms from residue A A1931: OP1  
Deleted the following atoms from residue A A1925: OP1  
Deleted the following atoms from residue A A1914: OP1  
Deleted the following atoms from residue A A1909: OP1  
Deleted the following atoms from residue A A1898: OP1  
Deleted the following atoms from residue A A1897: OP1  
Deleted the following atoms from residue A A1895: OP1  
Deleted the following atoms from residue A A1889: OP1  
Deleted the following atoms from residue A A1879: OP1  
Deleted the following atoms from residue A A1869: OP1  
Deleted the following atoms from residue A A1867: OP1  
Deleted the following atoms from residue A A1866: OP1  
Deleted the following atoms from residue A A1842: OP1  
Deleted the following atoms from residue A A1834: OP1  
Deleted the following atoms from residue A A1825: OP1  
Deleted the following atoms from residue A A1823: OP1  
Deleted the following atoms from residue A A1822: OP1  
Deleted the following atoms from residue A A1817: OP1  
Deleted the following atoms from residue A A1815: OP1  
Deleted the following atoms from residue A A1804: OP1  
Deleted the following atoms from residue A A1800: OP1  
Deleted the following atoms from residue A A1799: OP1  
Deleted the following atoms from residue A A1798: OP1  
Deleted the following atoms from residue A A1796: OP1  
Deleted the following atoms from residue A A1786: OP1  
Deleted the following atoms from residue A A1782: OP1  
Deleted the following atoms from residue A A1781: OP1  
Deleted the following atoms from residue A A1775: OP1  
Deleted the following atoms from residue A A1768: OP1  
Deleted the following atoms from residue A A1762: OP1  
Deleted the following atoms from residue A A1753: OP1  
Deleted the following atoms from residue A A1743: OP1  
Deleted the following atoms from residue A A1740: OP1  
Deleted the following atoms from residue A A1731: OP1  
Deleted the following atoms from residue A A1711: OP1  
Deleted the following atoms from residue A A1710: OP1  
Deleted the following atoms from residue A A1707: OP1  
Deleted the following atoms from residue A A1706: OP1  
Deleted the following atoms from residue A A1696: OP1  
Deleted the following atoms from residue A A1692: OP1  
Deleted the following atoms from residue A A1688: OP1  
Deleted the following atoms from residue A A1683: OP1  
Deleted the following atoms from residue A A1682: OP1  
Deleted the following atoms from residue A A1677: OP1  
Deleted the following atoms from residue A A1672: OP1  
Deleted the following atoms from residue A A1664: OP1  
Deleted the following atoms from residue A A1658: OP1  
Deleted the following atoms from residue A A1656: OP1  
Deleted the following atoms from residue A A1652: OP1  
Deleted the following atoms from residue A A1650: OP1  
Deleted the following atoms from residue A A1645: OP1  
Deleted the following atoms from residue A A1636: OP1  
Deleted the following atoms from residue A A1635: OP1  
Deleted the following atoms from residue A A1633: OP1  
Deleted the following atoms from residue A A1632: OP1  
Deleted the following atoms from residue A A1631: OP1  
Deleted the following atoms from residue A A1630: OP1  
Deleted the following atoms from residue A A1628: OP1  
Deleted the following atoms from residue A A1612: OP1  
Deleted the following atoms from residue A A1605: OP1  
Deleted the following atoms from residue A A1598: OP1  
Deleted the following atoms from residue A A1589: OP1  
Deleted the following atoms from residue A A1585: OP1  
Deleted the following atoms from residue A A1575: OP1  
Deleted the following atoms from residue A A1571: OP1  
Deleted the following atoms from residue A A1558: OP1  
Deleted the following atoms from residue A A1555: OP1  
Deleted the following atoms from residue A A1544: OP1  
Deleted the following atoms from residue A A1535: OP1  
Deleted the following atoms from residue A A1531: OP1  
Deleted the following atoms from residue A A1529: OP1  
Deleted the following atoms from residue A A1526: OP1  
Deleted the following atoms from residue A A1519: OP1  
Deleted the following atoms from residue A A1516: OP1  
Deleted the following atoms from residue A A1515: OP1  
Deleted the following atoms from residue A A1512: OP1  
Deleted the following atoms from residue A A1505: OP1  
Deleted the following atoms from residue A A1499: OP1  
Deleted the following atoms from residue A A1494: OP1  
Deleted the following atoms from residue A A1489: OP1  
Deleted the following atoms from residue A A1485: OP1  
Deleted the following atoms from residue A A1484: OP1  
Deleted the following atoms from residue A A1475: OP1  
Deleted the following atoms from residue A A1472: OP1  
Deleted the following atoms from residue A A1468: OP1  
Deleted the following atoms from residue A A1464: OP1  
Deleted the following atoms from residue A A1456: OP1  
Deleted the following atoms from residue A A1441: OP1  
Deleted the following atoms from residue A A1438: OP1  
Deleted the following atoms from residue A A1430: OP1  
Deleted the following atoms from residue A A1422: OP1  
Deleted the following atoms from residue A A1420: OP1  
Deleted the following atoms from residue A A1400: OP1  
Deleted the following atoms from residue A A1394: OP1  
Deleted the following atoms from residue A A1388: OP1  
Deleted the following atoms from residue A A1377: OP1  
Deleted the following atoms from residue A A1371: OP1  
Deleted the following atoms from residue A A1357: OP1  
Deleted the following atoms from residue A A1343: OP1  
Deleted the following atoms from residue A A1339: OP1  
Deleted the following atoms from residue A A1336: OP1  
Deleted the following atoms from residue A A1331: OP1  
Deleted the following atoms from residue A A1322: OP1  
Deleted the following atoms from residue A A1321: OP1  
Deleted the following atoms from residue A A1319: OP1  
Deleted the following atoms from residue A A1314: OP1  
Deleted the following atoms from residue A A1312: OP1  
Deleted the following atoms from residue A A1309: OP1  
Deleted the following atoms from residue A A1308: OP1  
Deleted the following atoms from residue A A1304: OP1  
Deleted the following atoms from residue A A1301: OP1  
Deleted the following atoms from residue A A1298: OP1  
Deleted the following atoms from residue A A1290: OP1  
Deleted the following atoms from residue A A1287: OP1  
Deleted the following atoms from residue A A1283: OP1  
Deleted the following atoms from residue A A1282: OP1  
Deleted the following atoms from residue A A1280: OP1  
Deleted the following atoms from residue A A1273: OP1  
Deleted the following atoms from residue A A1250: OP1  
Deleted the following atoms from residue A A1249: OP1  
Deleted the following atoms from residue A A1240: OP1  
Deleted the following atoms from residue A A1239: OP1  
Deleted the following atoms from residue A A1231: OP1  
Deleted the following atoms from residue A A1229: OP1  
Deleted the following atoms from residue A A1226: OP1  
Deleted the following atoms from residue A A1220: OP1  
Deleted the following atoms from residue A A1214: OP1  
Deleted the following atoms from residue A A1208: OP1  
Deleted the following atoms from residue A A1206: OP1  
Deleted the following atoms from residue A A1203: OP1  
Deleted the following atoms from residue A A1195: OP1  
Deleted the following atoms from residue A A1194: OP1  
Deleted the following atoms from residue A A1190: OP1  
Deleted the following atoms from residue A A1187: OP1  
Deleted the following atoms from residue A A1185: OP1  
Deleted the following atoms from residue A A1183: OP1  
Deleted the following atoms from residue A A1168: OP1  
Deleted the following atoms from residue A A1165: OP1  
Deleted the following atoms from residue A A1154: OP1  
Deleted the following atoms from residue A A1145: OP1  
Deleted the following atoms from residue A A1127: OP1  
Deleted the following atoms from residue A A1125: OP1  
Deleted the following atoms from residue A A1108: OP1  
Deleted the following atoms from residue A A1093: OP1  
Deleted the following atoms from residue A A1090: OP1  
Deleted the following atoms from residue A A1067: OP1  
Deleted the following atoms from residue A A1060: OP1  
Deleted the following atoms from residue A A1054: OP1  
Deleted the following atoms from residue A A1052: OP1  
Deleted the following atoms from residue A A1050: OP1  
Deleted the following atoms from residue A A1048: OP1  
Deleted the following atoms from residue A A1040: OP1  
Deleted the following atoms from residue A A1035: OP1  
Deleted the following atoms from residue A A1032: OP1  
Deleted the following atoms from residue A A1029: OP1  
Deleted the following atoms from residue A A1022: OP1  
Deleted the following atoms from residue A A1020: OP1  
Deleted the following atoms from residue A A1014: OP1  
Deleted the following atoms from residue A A1012: OP1  
Deleted the following atoms from residue A A1007: OP1  
Deleted the following atoms from residue A A1001: OP1  
Deleted the following atoms from residue A A998: OP1  
Deleted the following atoms from residue A A996: OP1  
Deleted the following atoms from residue A A992: OP1  
Deleted the following atoms from residue A A986: OP1  
Deleted the following atoms from residue A A967: OP1  
Deleted the following atoms from residue A A963: OP1  
Deleted the following atoms from residue A A958: OP1  
Deleted the following atoms from residue A A957: OP1  
Deleted the following atoms from residue A A950: OP1  
Deleted the following atoms from residue A A949: OP1  
Deleted the following atoms from residue A A947: OP1  
Deleted the following atoms from residue A A945: OP1  
Deleted the following atoms from residue A A941: OP1  
Deleted the following atoms from residue A A940: OP1  
Deleted the following atoms from residue A A936: OP1  
Deleted the following atoms from residue A A918: OP1  
Deleted the following atoms from residue A A915: OP1  
Deleted the following atoms from residue A A906: OP1  
Deleted the following atoms from residue A A903: OP1  
Deleted the following atoms from residue A A901: OP1  
Deleted the following atoms from residue A A893: OP1  
Deleted the following atoms from residue A A890: OP1  
Deleted the following atoms from residue A A889: OP1  
Deleted the following atoms from residue A A887: OP1  
Deleted the following atoms from residue A A882: OP1  
Deleted the following atoms from residue A A874: OP1  
Deleted the following atoms from residue A A862: OP1  
Deleted the following atoms from residue A A860: OP1  
Deleted the following atoms from residue A A841: OP1  
Deleted the following atoms from residue A A839: OP1  
Deleted the following atoms from residue A A833: OP1  
Deleted the following atoms from residue A A832: OP1  
Deleted the following atoms from residue A A822: OP1  
Deleted the following atoms from residue A A818: OP1  
Deleted the following atoms from residue A A803: OP1  
Deleted the following atoms from residue A A791: OP1  
Deleted the following atoms from residue A A789: OP1  
Deleted the following atoms from residue A A782: OP1  
Deleted the following atoms from residue A A774: OP1  
Deleted the following atoms from residue A A773: OP1  
Deleted the following atoms from residue A A769: OP1  
Deleted the following atoms from residue A A766: OP1  
Deleted the following atoms from residue A A761: OP1  
Deleted the following atoms from residue A A744: OP1  
Deleted the following atoms from residue A A732: OP1  
Deleted the following atoms from residue A A728: OP1  
Deleted the following atoms from residue A A719: OP1  
Deleted the following atoms from residue A A716: OP1  
Deleted the following atoms from residue A A715: OP1  
Deleted the following atoms from residue A A714: OP1  
Deleted the following atoms from residue A A709: OP1  
Deleted the following atoms from residue A A707: OP1  
Deleted the following atoms from residue A A701: OP1  
Deleted the following atoms from residue A A697: OP1  
Deleted the following atoms from residue A A682: OP1  
Deleted the following atoms from residue A A681: OP1  
Deleted the following atoms from residue A A671: OP1  
Deleted the following atoms from residue A A659: OP1  
Deleted the following atoms from residue A A655: OP1  
Deleted the following atoms from residue A A651: OP1  
Deleted the following atoms from residue A A645: OP1  
Deleted the following atoms from residue A A634: OP1  
Deleted the following atoms from residue A A629: OP1  
Deleted the following atoms from residue A A626: OP1  
Deleted the following atoms from residue A A622: OP1  
Deleted the following atoms from residue A A615: OP1  
Deleted the following atoms from residue A A611: OP1  
Deleted the following atoms from residue A A610: OP1  
Deleted the following atoms from residue A A608: OP1  
Deleted the following atoms from residue A A588: OP1  
Deleted the following atoms from residue A A574: OP1  
Deleted the following atoms from residue A A570: OP1  
Deleted the following atoms from residue A A569: OP1  
Deleted the following atoms from residue A A567: OP1  
Deleted the following atoms from residue A A566: OP1  
Deleted the following atoms from residue A A553: OP1  
Deleted the following atoms from residue A A551: OP1  
Deleted the following atoms from residue A A545: OP1  
Deleted the following atoms from residue A A543: OP1  
Deleted the following atoms from residue A A541: OP1  
Deleted the following atoms from residue A A539: OP1  
Deleted the following atoms from residue A A535: OP1  
Deleted the following atoms from residue A A530: OP1  
Deleted the following atoms from residue A A522: OP1  
Deleted the following atoms from residue A A519: OP1  
Deleted the following atoms from residue A A518: OP1  
Deleted the following atoms from residue A A517: OP1  
Deleted the following atoms from residue A A516: OP1  
Deleted the following atoms from residue A A510: OP1  
Deleted the following atoms from residue A A499: OP1  
Deleted the following atoms from residue A A496: OP1  
Deleted the following atoms from residue A A493: OP1  
Deleted the following atoms from residue A A488: OP1  
Deleted the following atoms from residue A A486: OP1  
Deleted the following atoms from residue A A482: OP1  
Deleted the following atoms from residue A A478: OP1  
Deleted the following atoms from residue A A469: OP1  
Deleted the following atoms from residue A A462: OP1  
Deleted the following atoms from residue A A461: OP1  
Deleted the following atoms from residue A A454: OP1  
Deleted the following atoms from residue A A441: OP1  
Deleted the following atoms from residue A A440: OP1  
Deleted the following atoms from residue A A430: OP1  
Deleted the following atoms from residue A A421: OP1  
Deleted the following atoms from residue A A420: OP1  
Deleted the following atoms from residue A A413: OP1  
Deleted the following atoms from residue A A410: OP1  
Deleted the following atoms from residue A A404: OP1  
Deleted the following atoms from residue A A401: OP1  
Deleted the following atoms from residue A A394: OP1  
Deleted the following atoms from residue A A392: OP1  
Deleted the following atoms from residue A A391: OP1  
Deleted the following atoms from residue A A389: OP1  
Deleted the following atoms from residue A A383: OP1  
Deleted the following atoms from residue A A382: OP1  
Deleted the following atoms from residue A A378: OP1  
Deleted the following atoms from residue A A376: OP1  
Deleted the following atoms from residue A A368: OP1  
Deleted the following atoms from residue A A367: OP1  
Deleted the following atoms from residue A A348: OP1  
Deleted the following atoms from residue A A347: OP1  
Deleted the following atoms from residue A A346: OP1  
Deleted the following atoms from residue A A339: OP1  
Deleted the following atoms from residue A A335: OP1  
Deleted the following atoms from residue A A328: OP1  
Deleted the following atoms from residue A A325: OP1  
Deleted the following atoms from residue A A317: OP1  
Deleted the following atoms from residue A A304: OP1  
Deleted the following atoms from residue A A301: OP1  
Deleted the following atoms from residue A A281: OP1  
Deleted the following atoms from residue A A280: OP1  
Deleted the following atoms from residue A A278: OP1  
Deleted the following atoms from residue A A277: OP1  
Deleted the following atoms from residue A A274: OP1  
Deleted the following atoms from residue A A272: OP1  
Deleted the following atoms from residue A A264: OP1  
Deleted the following atoms from residue A A259: OP1  
Deleted the following atoms from residue A A257: OP1  
Deleted the following atoms from residue A A253: OP1  
Deleted the following atoms from residue A A246: OP1  
Deleted the following atoms from residue A A235: OP1  
Deleted the following atoms from residue A A228: OP1  
Deleted the following atoms from residue A A227: OP1  
Deleted the following atoms from residue A A224: OP1  
Deleted the following atoms from residue A A223: OP1  
Deleted the following atoms from residue A A218: OP1  
Deleted the following atoms from residue A A215: OP1  
Deleted the following atoms from residue A A206: OP1  
Deleted the following atoms from residue A A201: OP1  
Deleted the following atoms from residue A A199: OP1  
Deleted the following atoms from residue A A198: OP1  
Deleted the following atoms from residue A A193: OP1  
Deleted the following atoms from residue A A192: OP1  
Deleted the following atoms from residue A A188: OP1  
Deleted the following atoms from residue A A182: OP1  
Deleted the following atoms from residue A A178: OP1  
Deleted the following atoms from residue A A176: OP1  
Deleted the following atoms from residue A A173: OP1  
Deleted the following atoms from residue A A166: OP1  
Deleted the following atoms from residue A A162: OP1  
Deleted the following atoms from residue A A161: OP1  
Deleted the following atoms from residue A A157: OP1  
Deleted the following atoms from residue A A147: OP1  
Deleted the following atoms from residue A A145: OP1  
Deleted the following atoms from residue A A133: OP1  
Deleted the following atoms from residue A A131: OP1  
Deleted the following atoms from residue A A130: OP1  
Deleted the following atoms from residue A A118: OP1  
Deleted the following atoms from residue A A117: OP1  
Deleted the following atoms from residue A A108: OP1  
Deleted the following atoms from residue A A106: OP1  
Deleted the following atoms from residue A A90: OP1  
Deleted the following atoms from residue A A67: OP1  
Deleted the following atoms from residue A A65: OP1  
Deleted the following atoms from residue A A64: OP1  
Deleted the following atoms from residue A A61: OP1  
Deleted the following atoms from residue A A56: OP1  
Deleted the following atoms from residue A A53: OP1  
Deleted the following atoms from residue A A44: OP1  
Deleted the following atoms from residue A A41: OP1  
Deleted the following atoms from residue A A38: OP1  
Deleted the following atoms from residue A A28: OP1  
Deleted the following atoms from residue A A21: OP1  
Deleted the following atoms from residue A A13: OP1  
Deleted the following atoms from residue A A10: OP1  
Deleted the following atoms from residue A A6: OP1  
Deleted the following atoms from residue A A5: OP1  
Deleted the following atoms from residue G A2722: OP1  
Deleted the following atoms from residue G A2263: OP1  
Deleted the following atoms from residue G A2183: OP1  
Deleted the following atoms from residue G A2182: OP1  
Deleted the following atoms from residue G A2181: OP1  
Deleted the following atoms from residue G A1863: OP1  
Deleted the following atoms from residue G A1862: OP1  
Deleted the following atoms from residue G A831: OP1  
Deleted the following atoms from residue G A448: OP1  
Deleted the following atoms from residue G A252: OP1  
Deleted the following atoms from residue U a1250: OP1  
Deleted the following atoms from residue U B54: OP1  
Deleted the following atoms from residue U A1644: OP1  
Deleted the following atoms from residue U A364: OP1  
Deleted the following atoms from residue C a1348: OP1  
Deleted the following atoms from residue C a398: OP1  
Deleted the following atoms from residue C A2477: OP1  
Deleted the following atoms from residue C A2126: OP1  
Deleted the following atoms from residue C A2007: OP1  
Deleted the following atoms from residue C A1908: OP1  
Deleted the following atoms from residue C A1907: OP1  
Deleted the following atoms from residue C A1906: OP1  
Deleted the following atoms from residue C A1839: OP1  
Deleted the following atoms from residue C A905: OP1  
Deleted the following atoms from residue C A458: OP1  

> select clear

> select clear

> select clear

> addh

Summary of feedback from adding hydrogens to
210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb #1.2  
---  
warnings | Not adding hydrogens to /A U 3 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /A G 1934 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A U 1953 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A G 2265 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A G 2459 P because it is missing heavy-atom bond
partners  
5 messages similar to the above omitted  
Unknown hybridization for atom (P) of residue type MA6; not adding hydrogens
to it  
/E HOH 3222 O has bad number of bonds (3)  
notes | No usable SEQRES records for
210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb (#1.2) chain 0; guessing termini
instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 1; guessing termini instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 2; guessing termini instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 3; guessing termini instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 4; guessing termini instead  
48 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /0 MET 1, /3 MET 1, /5 MET
1, /6 MET 1, /7 PRO 2, /8 MET 1, /A U 3, /B G 2, /D G 2, /I PRO 2, /M MET 1,
/N MET 1, /O MET 1, /R MET 1, /U MET 1, /W MET 1, /X MET 1, /a G 9, /b G 1, /h
PRO 2, /m PRO 2, /u PRO 2  
Chain-initial residues that are not actual N termini: /1 LYS 2, /2 ALA 2, /4
ALA 2, /A C 287, /A A 1582, /F LYS 3, /G ALA 2, /H LYS 3, /J ASN 2, /K SER 2,
/P LEU 2, /Q SER 2, /S ASN 2, /T ALA 2, /V ILE 5, /Y SER 20, /Z ALA 2, /a A
111, /a G 240, /a G 1547, /b A 13, /c ILE 4, /d GLY 2, /e SER 2, /f TYR 3, /g
ASP 4, /i VAL 2, /j VAL 4, /k ILE 6, /l LYS 14, /n ARG 3, /o ALA 2, /p SER 4,
/q ALA 2, /r ARG 5, /s VAL 14, /t GLY 2  
Chain-final residues that are actual C termini: /2 GLU 58, /3 LEU 80, /5 THR
48, /7 MET 65, /8 GLY 38, /A C 2910, /B G 115, /D A 77, /F SER 228, /I LEU
206, /K LYS 175, /N LEU 122, /O ILE 146, /P GLU 135, /Q VAL 126, /R PHE 118,
/S ARG 115, /V LYS 115, /X LEU 101, /Y VAL 93, /a U 1567, /b A 19, /e GLN 201,
/g GLU 99, /i TRP 132, /l VAL 129, /o TRP 61, /p ARG 88, /q ASN 88, /s SER 76  
Chain-final residues that are not actual C termini: /0 ASN 534, /1 GLN 60, /4
VAL 54, /6 ALA 44, /A G 282, /A U 1578, /G THR 275, /H ALA 208, /J GLN 178, /M
ILE 147, /T LYS 119, /U ASN 101, /W LEU 91, /Z VAL 62, /a U 76, /a U 235, /a
MA6 1545, /b U 6, /c ASN 225, /d ILE 206, /f ILE 165, /h TYR 154, /j ARG 130,
/k LYS 101, /m PRO 135, /n VAL 116, /r GLU 84, /t HIS 83, /u ALA 82  
19170 hydrogen bonds  
/0 ASN 534 is not terminus, removing H atom from 'C'  
/1 GLN 60 is not terminus, removing H atom from 'C'  
/4 VAL 54 is not terminus, removing H atom from 'C'  
/6 ALA 44 is not terminus, removing H atom from 'C'  
/G THR 275 is not terminus, removing H atom from 'C'  
18 messages similar to the above omitted  
110 hydrogens added  
  
Deleted the following atoms from residue PUT a1717: H13, H24, H2, H23, H3  
Failed to add atoms ['H23'] to atom N1 because this will lead to having 5
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_PUT). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Deleted the following atoms from residue SCM a1718: HN2, HN3  
Failed to add atoms ['H23'] to atom N1 because this will lead to having 5
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (MC_PUT). If this template is
built into ISOLDE, please report this using Help/Report a bug  

> select clear

> addh

Summary of feedback from adding hydrogens to
210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb #1.2  
---  
warnings | Not adding hydrogens to /A U 3 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /A G 1934 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A U 1953 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A G 2265 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A G 2459 P because it is missing heavy-atom bond
partners  
5 messages similar to the above omitted  
Unknown hybridization for atom (P) of residue type MA6; not adding hydrogens
to it  
/E HOH 3222 O has bad number of bonds (3)  
notes | No usable SEQRES records for
210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb (#1.2) chain 0; guessing termini
instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 1; guessing termini instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 2; guessing termini instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 3; guessing termini instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 4; guessing termini instead  
48 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /0 MET 1, /3 MET 1, /5 MET
1, /6 MET 1, /7 PRO 2, /8 MET 1, /A U 3, /B G 2, /D G 2, /I PRO 2, /M MET 1,
/N MET 1, /O MET 1, /R MET 1, /U MET 1, /W MET 1, /X MET 1, /a G 9, /b G 1, /h
PRO 2, /m PRO 2, /u PRO 2  
Chain-initial residues that are not actual N termini: /1 LYS 2, /2 ALA 2, /4
ALA 2, /A C 287, /A A 1582, /F LYS 3, /G ALA 2, /H LYS 3, /J ASN 2, /K SER 2,
/P LEU 2, /Q SER 2, /S ASN 2, /T ALA 2, /V ILE 5, /Y SER 20, /Z ALA 2, /a A
111, /a G 240, /a G 1547, /b A 13, /c ILE 4, /d GLY 2, /e SER 2, /f TYR 3, /g
ASP 4, /i VAL 2, /j VAL 4, /k ILE 6, /l LYS 14, /n ARG 3, /o ALA 2, /p SER 4,
/q ALA 2, /r ARG 5, /s VAL 14, /t GLY 2  
Chain-final residues that are actual C termini: /2 GLU 58, /3 LEU 80, /5 THR
48, /7 MET 65, /8 GLY 38, /A C 2910, /B G 115, /D A 77, /F SER 228, /I LEU
206, /K LYS 175, /N LEU 122, /O ILE 146, /P GLU 135, /Q VAL 126, /R PHE 118,
/S ARG 115, /V LYS 115, /X LEU 101, /Y VAL 93, /a U 1567, /b A 19, /e GLN 201,
/g GLU 99, /i TRP 132, /l VAL 129, /o TRP 61, /p ARG 88, /q ASN 88, /s SER 76  
Chain-final residues that are not actual C termini: /0 ASN 534, /1 GLN 60, /4
VAL 54, /6 ALA 44, /A G 282, /A U 1578, /G THR 275, /H ALA 208, /J GLN 178, /M
ILE 147, /T LYS 119, /U ASN 101, /W LEU 91, /Z VAL 62, /a U 76, /a U 235, /a
MA6 1545, /b U 6, /c ASN 225, /d ILE 206, /f ILE 165, /h TYR 154, /j ARG 130,
/k LYS 101, /m PRO 135, /n VAL 116, /r GLU 84, /t HIS 83, /u ALA 82  
19171 hydrogen bonds  
/0 ASN 534 is not terminus, removing H atom from 'C'  
/1 GLN 60 is not terminus, removing H atom from 'C'  
/4 VAL 54 is not terminus, removing H atom from 'C'  
/6 ALA 44 is not terminus, removing H atom from 'C'  
/G THR 275 is not terminus, removing H atom from 'C'  
18 messages similar to the above omitted  
3 hydrogens added  
  

> select clear

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select up

10797 atoms, 7195 bonds, 3602 residues, 1 model selected  

> select down

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

Deleted the following atoms from residue PUT a1717: HN23  

> addh

Summary of feedback from adding hydrogens to
210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb #1.2  
---  
warnings | Not adding hydrogens to /A U 3 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /A G 1934 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A U 1953 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A G 2265 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A G 2459 P because it is missing heavy-atom bond
partners  
5 messages similar to the above omitted  
Unknown hybridization for atom (P) of residue type MA6; not adding hydrogens
to it  
notes | No usable SEQRES records for
210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb (#1.2) chain 0; guessing termini
instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 1; guessing termini instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 2; guessing termini instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 3; guessing termini instead  
No usable SEQRES records for 210616_70S-PoxtA_j223-ISOLDE_03.updated.pdb
(#1.2) chain 4; guessing termini instead  
48 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /0 MET 1, /3 MET 1, /5 MET
1, /6 MET 1, /7 PRO 2, /8 MET 1, /A U 3, /B G 2, /D G 2, /I PRO 2, /M MET 1,
/N MET 1, /O MET 1, /R MET 1, /U MET 1, /W MET 1, /X MET 1, /a G 9, /b G 1, /h
PRO 2, /m PRO 2, /u PRO 2  
Chain-initial residues that are not actual N termini: /1 LYS 2, /2 ALA 2, /4
ALA 2, /A C 287, /A A 1582, /F LYS 3, /G ALA 2, /H LYS 3, /J ASN 2, /K SER 2,
/P LEU 2, /Q SER 2, /S ASN 2, /T ALA 2, /V ILE 5, /Y SER 20, /Z ALA 2, /a A
111, /a G 240, /a G 1547, /b A 13, /c ILE 4, /d GLY 2, /e SER 2, /f TYR 3, /g
ASP 4, /i VAL 2, /j VAL 4, /k ILE 6, /l LYS 14, /n ARG 3, /o ALA 2, /p SER 4,
/q ALA 2, /r ARG 5, /s VAL 14, /t GLY 2  
Chain-final residues that are actual C termini: /2 GLU 58, /3 LEU 80, /5 THR
48, /7 MET 65, /8 GLY 38, /A C 2910, /B G 115, /D A 77, /F SER 228, /I LEU
206, /K LYS 175, /N LEU 122, /O ILE 146, /P GLU 135, /Q VAL 126, /R PHE 118,
/S ARG 115, /V LYS 115, /X LEU 101, /Y VAL 93, /a U 1567, /b A 19, /e GLN 201,
/g GLU 99, /i TRP 132, /l VAL 129, /o TRP 61, /p ARG 88, /q ASN 88, /s SER 76  
Chain-final residues that are not actual C termini: /0 ASN 534, /1 GLN 60, /4
VAL 54, /6 ALA 44, /A G 282, /A U 1578, /G THR 275, /H ALA 208, /J GLN 178, /M
ILE 147, /T LYS 119, /U ASN 101, /W LEU 91, /Z VAL 62, /a U 76, /a U 235, /a
MA6 1545, /b U 6, /c ASN 225, /d ILE 206, /f ILE 165, /h TYR 154, /j ARG 130,
/k LYS 101, /m PRO 135, /n VAL 116, /r GLU 84, /t HIS 83, /u ALA 82  
19171 hydrogen bonds  
/0 ASN 534 is not terminus, removing H atom from 'C'  
/1 GLN 60 is not terminus, removing H atom from 'C'  
/4 VAL 54 is not terminus, removing H atom from 'C'  
/6 ALA 44 is not terminus, removing H atom from 'C'  
/G THR 275 is not terminus, removing H atom from 'C'  
18 messages similar to the above omitted  
0 hydrogens added  
  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  




OpenGL version: 4.1 ATI-4.5.14
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.7 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 32 GB
      System Firmware Version: 1554.120.15.0.0
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 3:40

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP 24f:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 3CM9460GP9   
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 0.00

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.4
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.4
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.0
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.1.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Cc: Eric Pettersen added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: possible error in MD template

Reported by Caillan Crowe-McAuliffe

comment:2 by Tristan Croll, 4 years ago

Status: assigned → feedback

The template for PUT is fine (just checked). My guess as to what's causing your problem is that the putrescine is covalently bonded to another residue via N1? I'm afraid that new (i.e. not already built-in) covalent bonds between residues is one thing that isn't yet supported in ISOLDE (although I'm in discussions about how to make it possible). My general advice for situations like this is to model it as free putrescine, but add a strong (~5000 kJ/mol/A2) distance restraint in place of the covalent bond using ISOLDE's Rebuild tab. The result will be a little wonky and somewhat unsatisfying in ISOLDE itself, but as long as the density is reasonable things should stay under control sufficiently to allow your final refinement to correct the geometry.

comment:3 by Tristan Croll, 4 years ago

Resolution: → limitation
Status: feedback → closed

Response from Caillan: "Hi, thanks so much for checking the template and also for the advice. It is very helpful!"

Hopefully I'll be able to start making inroads into this in the coming year.

Note: See TracTickets for help on using tickets.